Diff for /imach/src/imach.c between versions 1.7 and 1.74

version 1.7, 2001/05/02 17:50:24 version 1.74, 2003/05/02 18:51:41
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************             Interpolated Markov Chain
   This program computes Healthy Life Expectancies from cross-longitudinal  
   data. Cross-longitudinal consist in a first survey ("cross") where    Short summary of the programme:
   individuals from different ages are interviewed on their health status    
   or degree of  disability. At least a second wave of interviews    This program computes Healthy Life Expectancies from
   ("longitudinal") should  measure each new individual health status.    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   Health expectancies are computed from the transistions observed between    first survey ("cross") where individuals from different ages are
   waves and are computed for each degree of severity of disability (number    interviewed on their health status or degree of disability (in the
   of life states). More degrees you consider, more time is necessary to    case of a health survey which is our main interest) -2- at least a
   reach the Maximum Likelihood of the parameters involved in the model.    second wave of interviews ("longitudinal") which measure each change
   The simplest model is the multinomial logistic model where pij is    (if any) in individual health status.  Health expectancies are
   the probabibility to be observed in state j at the second wave conditional    computed from the time spent in each health state according to a
   to be observed in state i at the first wave. Therefore the model is:    model. More health states you consider, more time is necessary to reach the
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Maximum Likelihood of the parameters involved in the model.  The
   is a covariate. If you want to have a more complex model than "constant and    simplest model is the multinomial logistic model where pij is the
   age", you should modify the program where the markup    probability to be observed in state j at the second wave
     *Covariates have to be included here again* invites you to do it.    conditional to be observed in state i at the first wave. Therefore
   More covariates you add, less is the speed of the convergence.    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     'age' is age and 'sex' is a covariate. If you want to have a more
   The advantage that this computer programme claims, comes from that if the    complex model than "constant and age", you should modify the program
   delay between waves is not identical for each individual, or if some    where the markup *Covariates have to be included here again* invites
   individual missed an interview, the information is not rounded or lost, but    you to do it.  More covariates you add, slower the
   taken into account using an interpolation or extrapolation.    convergence.
   hPijx is the probability to be  
   observed in state i at age x+h conditional to the observed state i at age    The advantage of this computer programme, compared to a simple
   x. The delay 'h' can be split into an exact number (nh*stepm) of    multinomial logistic model, is clear when the delay between waves is not
   unobserved intermediate  states. This elementary transition (by month or    identical for each individual. Also, if a individual missed an
   quarter trimester, semester or year) is model as a multinomial logistic.    intermediate interview, the information is lost, but taken into
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    account using an interpolation or extrapolation.  
   and the contribution of each individual to the likelihood is simply hPijx.  
     hPijx is the probability to be observed in state i at age x+h
   Also this programme outputs the covariance matrix of the parameters but also    conditional to the observed state i at age x. The delay 'h' can be
   of the life expectancies. It also computes the prevalence limits.    split into an exact number (nh*stepm) of unobserved intermediate
      states. This elementary transition (by month, quarter,
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    semester or year) is modelled as a multinomial logistic.  The hPx
            Institut national d'études démographiques, Paris.    matrix is simply the matrix product of nh*stepm elementary matrices
   This software have been partly granted by Euro-REVES, a concerted action    and the contribution of each individual to the likelihood is simply
   from the European Union.    hPijx.
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Also this programme outputs the covariance matrix of the parameters but also
   can be accessed at http://euroreves.ined.fr/imach .    of the life expectancies. It also computes the stable prevalence. 
   **********************************************************************/    
      Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #include <math.h>             Institut national d'études démographiques, Paris.
 #include <stdio.h>    This software have been partly granted by Euro-REVES, a concerted action
 #include <stdlib.h>    from the European Union.
 #include <unistd.h>    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 #define MAXLINE 256    can be accessed at http://euroreves.ined.fr/imach .
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #define windows    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    **********************************************************************/
   /*
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    main
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    read parameterfile
     read datafile
 #define NINTERVMAX 8    concatwav
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    if (mle >= 1)
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */      mlikeli
 #define NCOVMAX 8 /* Maximum number of covariates */    print results files
 #define MAXN 20000    if mle==1 
 #define YEARM 12. /* Number of months per year */       computes hessian
 #define AGESUP 130    read end of parameter file: agemin, agemax, bage, fage, estepm
 #define AGEBASE 40        begin-prev-date,...
     open gnuplot file
     open html file
 int nvar;    stable prevalence
 static int cptcov;     for age prevalim()
 int cptcovn, cptcovage=0, cptcoveff=0;    h Pij x
 int npar=NPARMAX;    variance of p varprob
 int nlstate=2; /* Number of live states */    forecasting if prevfcast==1 prevforecast call prevalence()
 int ndeath=1; /* Number of dead states */    health expectancies
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Variance-covariance of DFLE
     prevalence()
 int *wav; /* Number of waves for this individuual 0 is possible */     movingaverage()
 int maxwav; /* Maxim number of waves */    varevsij() 
 int mle, weightopt;    if popbased==1 varevsij(,popbased)
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    total life expectancies
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Variance of stable prevalence
 double **oldm, **newm, **savm; /* Working pointers to matrices */   end
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;  
 FILE *ficgp, *fichtm;  
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];   
  FILE  *ficresvij;  #include <math.h>
   char fileresv[FILENAMELENGTH];  #include <stdio.h>
  FILE  *ficresvpl;  #include <stdlib.h>
   char fileresvpl[FILENAMELENGTH];  #include <unistd.h>
   
 #define NR_END 1  #define MAXLINE 256
 #define FREE_ARG char*  #define GNUPLOTPROGRAM "gnuplot"
 #define FTOL 1.0e-10  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 80
 #define NRANSI  /*#define DEBUG*/
 #define ITMAX 200  #define windows
   #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define TOL 2.0e-4  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 #define CGOLD 0.3819660  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define ZEPS 1.0e-10  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
   #define NINTERVMAX 8
 #define GOLD 1.618034  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define GLIMIT 100.0  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define TINY 1.0e-20  #define NCOVMAX 8 /* Maximum number of covariates */
   #define MAXN 20000
 static double maxarg1,maxarg2;  #define YEARM 12. /* Number of months per year */
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  #define AGESUP 130
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  #define AGEBASE 40
    #ifdef windows
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #define DIRSEPARATOR '\\'
 #define rint(a) floor(a+0.5)  #define ODIRSEPARATOR '/'
   #else
 static double sqrarg;  #define DIRSEPARATOR '/'
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define ODIRSEPARATOR '\\'
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  #endif
   
 int imx;  char version[80]="Imach version 0.95, February 2003, INED-EUROREVES ";
 int stepm;  int erreur; /* Error number */
 /* Stepm, step in month: minimum step interpolation*/  int nvar;
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int m,nb;  int npar=NPARMAX;
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  int nlstate=2; /* Number of live states */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  int ndeath=1; /* Number of dead states */
 double **pmmij;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
 double *weight;  
 int **s; /* Status */  int *wav; /* Number of waves for this individuual 0 is possible */
 double *agedc, **covar, idx;  int maxwav; /* Maxim number of waves */
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  int jmin, jmax; /* min, max spacing between 2 waves */
   int mle, weightopt;
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 double ftolhess; /* Tolerance for computing hessian */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 /**************** split *************************/             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 static  int split( char *path, char *dirc, char *name )  double jmean; /* Mean space between 2 waves */
 {  double **oldm, **newm, **savm; /* Working pointers to matrices */
    char *s;                             /* pointer */  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
    int  l1, l2;                         /* length counters */  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog;
    l1 = strlen( path );                 /* length of path */  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  FILE *ficresprobmorprev;
    s = strrchr( path, '\\' );           /* find last / */  FILE *fichtm; /* Html File */
    if ( s == NULL ) {                   /* no directory, so use current */  FILE *ficreseij;
 #if     defined(__bsd__)                /* get current working directory */  char filerese[FILENAMELENGTH];
       extern char       *getwd( );  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
       if ( getwd( dirc ) == NULL ) {  FILE  *ficresvpl;
 #else  char fileresvpl[FILENAMELENGTH];
       extern char       *getcwd( );  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 #endif  
          return( GLOCK_ERROR_GETCWD );  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       }  char filelog[FILENAMELENGTH]; /* Log file */
       strcpy( name, path );             /* we've got it */  char filerest[FILENAMELENGTH];
    } else {                             /* strip direcotry from path */  char fileregp[FILENAMELENGTH];
       s++;                              /* after this, the filename */  char popfile[FILENAMELENGTH];
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define NR_END 1
       dirc[l1-l2] = 0;                  /* add zero */  #define FREE_ARG char*
    }  #define FTOL 1.0e-10
    l1 = strlen( dirc );                 /* length of directory */  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #define NRANSI 
    return( 0 );                         /* we're done */  #define ITMAX 200 
 }  
   #define TOL 2.0e-4 
   
 /******************************************/  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 void replace(char *s, char*t)  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 {  
   int i;  #define GOLD 1.618034 
   int lg=20;  #define GLIMIT 100.0 
   i=0;  #define TINY 1.0e-20 
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {  static double maxarg1,maxarg2;
     (s[i] = t[i]);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     if (t[i]== '\\') s[i]='/';  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   }    
 }  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
 int nbocc(char *s, char occ)  
 {  static double sqrarg;
   int i,j=0;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   int lg=20;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   i=0;  
   lg=strlen(s);  int imx; 
   for(i=0; i<= lg; i++) {  int stepm;
   if  (s[i] == occ ) j++;  /* Stepm, step in month: minimum step interpolation*/
   }  
   return j;  int estepm;
 }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
 void cutv(char *u,char *v, char*t, char occ)  int m,nb;
 {  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   int i,lg,j,p=0;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   i=0;  double **pmmij, ***probs;
   for(j=0; j<=strlen(t)-1; j++) {  double dateintmean=0;
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }  double *weight;
   int **s; /* Status */
   lg=strlen(t);  double *agedc, **covar, idx;
   for(j=0; j<p; j++) {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
     (u[j] = t[j]);  
   }  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
      u[p]='\0';  double ftolhess; /* Tolerance for computing hessian */
   
    for(j=0; j<= lg; j++) {  /**************** split *************************/
     if (j>=(p+1))(v[j-p-1] = t[j]);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   }  {
 }    char  *ss;                            /* pointer */
     int   l1, l2;                         /* length counters */
 /********************** nrerror ********************/  
     l1 = strlen(path );                   /* length of path */
 void nrerror(char error_text[])    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   fprintf(stderr,"ERREUR ...\n");    if ( ss == NULL ) {                   /* no directory, so use current */
   fprintf(stderr,"%s\n",error_text);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   exit(1);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 }      /* get current working directory */
 /*********************** vector *******************/      /*    extern  char* getcwd ( char *buf , int len);*/
 double *vector(int nl, int nh)      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 {        return( GLOCK_ERROR_GETCWD );
   double *v;      }
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));      strcpy( name, path );               /* we've got it */
   if (!v) nrerror("allocation failure in vector");    } else {                              /* strip direcotry from path */
   return v-nl+NR_END;      ss++;                               /* after this, the filename */
 }      l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 /************************ free vector ******************/      strcpy( name, ss );         /* save file name */
 void free_vector(double*v, int nl, int nh)      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 {      dirc[l1-l2] = 0;                    /* add zero */
   free((FREE_ARG)(v+nl-NR_END));    }
 }    l1 = strlen( dirc );                  /* length of directory */
   #ifdef windows
 /************************ivector *******************************/    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 int *ivector(long nl,long nh)  #else
 {    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   int *v;  #endif
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    ss = strrchr( name, '.' );            /* find last / */
   if (!v) nrerror("allocation failure in ivector");    ss++;
   return v-nl+NR_END;    strcpy(ext,ss);                       /* save extension */
 }    l1= strlen( name);
     l2= strlen(ss)+1;
 /******************free ivector **************************/    strncpy( finame, name, l1-l2);
 void free_ivector(int *v, long nl, long nh)    finame[l1-l2]= 0;
 {    return( 0 );                          /* we're done */
   free((FREE_ARG)(v+nl-NR_END));  }
 }  
   
 /******************* imatrix *******************************/  /******************************************/
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  void replace(char *s, char*t)
 {  {
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    int i;
   int **m;    int lg=20;
      i=0;
   /* allocate pointers to rows */    lg=strlen(t);
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    for(i=0; i<= lg; i++) {
   if (!m) nrerror("allocation failure 1 in matrix()");      (s[i] = t[i]);
   m += NR_END;      if (t[i]== '\\') s[i]='/';
   m -= nrl;    }
    }
    
   /* allocate rows and set pointers to them */  int nbocc(char *s, char occ)
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    int i,j=0;
   m[nrl] += NR_END;    int lg=20;
   m[nrl] -= ncl;    i=0;
      lg=strlen(s);
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    for(i=0; i<= lg; i++) {
      if  (s[i] == occ ) j++;
   /* return pointer to array of pointers to rows */    }
   return m;    return j;
 }  }
   
 /****************** free_imatrix *************************/  void cutv(char *u,char *v, char*t, char occ)
 void free_imatrix(m,nrl,nrh,ncl,nch)  {
       int **m;    /* cuts string t into u and v where u is ended by char occ excluding it
       long nch,ncl,nrh,nrl;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
      /* free an int matrix allocated by imatrix() */       gives u="abcedf" and v="ghi2j" */
 {    int i,lg,j,p=0;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    i=0;
   free((FREE_ARG) (m+nrl-NR_END));    for(j=0; j<=strlen(t)-1; j++) {
 }      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     }
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    lg=strlen(t);
 {    for(j=0; j<p; j++) {
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;      (u[j] = t[j]);
   double **m;    }
        u[p]='\0';
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");     for(j=0; j<= lg; j++) {
   m += NR_END;      if (j>=(p+1))(v[j-p-1] = t[j]);
   m -= nrl;    }
   }
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /********************** nrerror ********************/
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  void nrerror(char error_text[])
   {
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    fprintf(stderr,"ERREUR ...\n");
   return m;    fprintf(stderr,"%s\n",error_text);
 }    exit(EXIT_FAILURE);
   }
 /*************************free matrix ************************/  /*********************** vector *******************/
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  double *vector(int nl, int nh)
 {  {
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    double *v;
   free((FREE_ARG)(m+nrl-NR_END));    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 }    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
 /******************* ma3x *******************************/  }
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {  /************************ free vector ******************/
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  void free_vector(double*v, int nl, int nh)
   double ***m;  {
     free((FREE_ARG)(v+nl-NR_END));
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  }
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  /************************ivector *******************************/
   m -= nrl;  int *ivector(long nl,long nh)
   {
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    int *v;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   m[nrl] += NR_END;    if (!v) nrerror("allocation failure in ivector");
   m[nrl] -= ncl;    return v-nl+NR_END;
   }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   /******************free ivector **************************/
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  void free_ivector(int *v, long nl, long nh)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  {
   m[nrl][ncl] += NR_END;    free((FREE_ARG)(v+nl-NR_END));
   m[nrl][ncl] -= nll;  }
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;  /******************* imatrix *******************************/
    int **imatrix(long nrl, long nrh, long ncl, long nch) 
   for (i=nrl+1; i<=nrh; i++) {       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  { 
     for (j=ncl+1; j<=nch; j++)    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       m[i][j]=m[i][j-1]+nlay;    int **m; 
   }    
   return m;    /* allocate pointers to rows */ 
 }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
 /*************************free ma3x ************************/    m += NR_END; 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    m -= nrl; 
 {    
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    /* allocate rows and set pointers to them */ 
   free((FREE_ARG)(m+nrl-NR_END));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     m[nrl] += NR_END; 
 /***************** f1dim *************************/    m[nrl] -= ncl; 
 extern int ncom;    
 extern double *pcom,*xicom;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 extern double (*nrfunc)(double []);    
      /* return pointer to array of pointers to rows */ 
 double f1dim(double x)    return m; 
 {  } 
   int j;  
   double f;  /****************** free_imatrix *************************/
   double *xt;  void free_imatrix(m,nrl,nrh,ncl,nch)
          int **m;
   xt=vector(1,ncom);        long nch,ncl,nrh,nrl; 
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];       /* free an int matrix allocated by imatrix() */ 
   f=(*nrfunc)(xt);  { 
   free_vector(xt,1,ncom);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   return f;    free((FREE_ARG) (m+nrl-NR_END)); 
 }  } 
   
 /*****************brent *************************/  /******************* matrix *******************************/
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  double **matrix(long nrl, long nrh, long ncl, long nch)
 {  {
   int iter;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   double a,b,d,etemp;    double **m;
   double fu,fv,fw,fx;  
   double ftemp;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double p,q,r,tol1,tol2,u,v,w,x,xm;    if (!m) nrerror("allocation failure 1 in matrix()");
   double e=0.0;    m += NR_END;
      m -= nrl;
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   x=w=v=bx;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   fw=fv=fx=(*f)(x);    m[nrl] += NR_END;
   for (iter=1;iter<=ITMAX;iter++) {    m[nrl] -= ncl;
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    return m;
     printf(".");fflush(stdout);    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
 #ifdef DEBUG     */
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  }
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif  /*************************free matrix ************************/
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       *xmin=x;  {
       return fx;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     }    free((FREE_ARG)(m+nrl-NR_END));
     ftemp=fu;  }
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);  /******************* ma3x *******************************/
       q=(x-v)*(fx-fw);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       p=(x-v)*q-(x-w)*r;  {
       q=2.0*(q-r);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       if (q > 0.0) p = -p;    double ***m;
       q=fabs(q);  
       etemp=e;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       e=d;    if (!m) nrerror("allocation failure 1 in matrix()");
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    m += NR_END;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    m -= nrl;
       else {  
         d=p/q;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         u=x+d;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         if (u-a < tol2 || b-u < tol2)    m[nrl] += NR_END;
           d=SIGN(tol1,xm-x);    m[nrl] -= ncl;
       }  
     } else {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     fu=(*f)(u);    m[nrl][ncl] += NR_END;
     if (fu <= fx) {    m[nrl][ncl] -= nll;
       if (u >= x) a=x; else b=x;    for (j=ncl+1; j<=nch; j++) 
       SHFT(v,w,x,u)      m[nrl][j]=m[nrl][j-1]+nlay;
         SHFT(fv,fw,fx,fu)    
         } else {    for (i=nrl+1; i<=nrh; i++) {
           if (u < x) a=u; else b=u;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
           if (fu <= fw || w == x) {      for (j=ncl+1; j<=nch; j++) 
             v=w;        m[i][j]=m[i][j-1]+nlay;
             w=u;    }
             fv=fw;    return m; 
             fw=fu;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
           } else if (fu <= fv || v == x || v == w) {             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
             v=u;    */
             fv=fu;  }
           }  
         }  /*************************free ma3x ************************/
   }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   nrerror("Too many iterations in brent");  {
   *xmin=x;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   return fx;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 }    free((FREE_ARG)(m+nrl-NR_END));
   }
 /****************** mnbrak ***********************/  
   /***************** f1dim *************************/
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  extern int ncom; 
             double (*func)(double))  extern double *pcom,*xicom;
 {  extern double (*nrfunc)(double []); 
   double ulim,u,r,q, dum;   
   double fu;  double f1dim(double x) 
    { 
   *fa=(*func)(*ax);    int j; 
   *fb=(*func)(*bx);    double f;
   if (*fb > *fa) {    double *xt; 
     SHFT(dum,*ax,*bx,dum)   
       SHFT(dum,*fb,*fa,dum)    xt=vector(1,ncom); 
       }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   *cx=(*bx)+GOLD*(*bx-*ax);    f=(*nrfunc)(xt); 
   *fc=(*func)(*cx);    free_vector(xt,1,ncom); 
   while (*fb > *fc) {    return f; 
     r=(*bx-*ax)*(*fb-*fc);  } 
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  /*****************brent *************************/
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     ulim=(*bx)+GLIMIT*(*cx-*bx);  { 
     if ((*bx-u)*(u-*cx) > 0.0) {    int iter; 
       fu=(*func)(u);    double a,b,d,etemp;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    double fu,fv,fw,fx;
       fu=(*func)(u);    double ftemp;
       if (fu < *fc) {    double p,q,r,tol1,tol2,u,v,w,x,xm; 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    double e=0.0; 
           SHFT(*fb,*fc,fu,(*func)(u))   
           }    a=(ax < cx ? ax : cx); 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    b=(ax > cx ? ax : cx); 
       u=ulim;    x=w=v=bx; 
       fu=(*func)(u);    fw=fv=fx=(*f)(x); 
     } else {    for (iter=1;iter<=ITMAX;iter++) { 
       u=(*cx)+GOLD*(*cx-*bx);      xm=0.5*(a+b); 
       fu=(*func)(u);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     SHFT(*ax,*bx,*cx,u)      printf(".");fflush(stdout);
       SHFT(*fa,*fb,*fc,fu)      fprintf(ficlog,".");fflush(ficlog);
       }  #ifdef DEBUG
 }      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 /*************** linmin ************************/      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   #endif
 int ncom;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 double *pcom,*xicom;        *xmin=x; 
 double (*nrfunc)(double []);        return fx; 
        } 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      ftemp=fu;
 {      if (fabs(e) > tol1) { 
   double brent(double ax, double bx, double cx,        r=(x-w)*(fx-fv); 
                double (*f)(double), double tol, double *xmin);        q=(x-v)*(fx-fw); 
   double f1dim(double x);        p=(x-v)*q-(x-w)*r; 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,        q=2.0*(q-r); 
               double *fc, double (*func)(double));        if (q > 0.0) p = -p; 
   int j;        q=fabs(q); 
   double xx,xmin,bx,ax;        etemp=e; 
   double fx,fb,fa;        e=d; 
          if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   ncom=n;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   pcom=vector(1,n);        else { 
   xicom=vector(1,n);          d=p/q; 
   nrfunc=func;          u=x+d; 
   for (j=1;j<=n;j++) {          if (u-a < tol2 || b-u < tol2) 
     pcom[j]=p[j];            d=SIGN(tol1,xm-x); 
     xicom[j]=xi[j];        } 
   }      } else { 
   ax=0.0;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   xx=1.0;      } 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      fu=(*f)(u); 
 #ifdef DEBUG      if (fu <= fx) { 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);        if (u >= x) a=x; else b=x; 
 #endif        SHFT(v,w,x,u) 
   for (j=1;j<=n;j++) {          SHFT(fv,fw,fx,fu) 
     xi[j] *= xmin;          } else { 
     p[j] += xi[j];            if (u < x) a=u; else b=u; 
   }            if (fu <= fw || w == x) { 
   free_vector(xicom,1,n);              v=w; 
   free_vector(pcom,1,n);              w=u; 
 }              fv=fw; 
               fw=fu; 
 /*************** powell ************************/            } else if (fu <= fv || v == x || v == w) { 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,              v=u; 
             double (*func)(double []))              fv=fu; 
 {            } 
   void linmin(double p[], double xi[], int n, double *fret,          } 
               double (*func)(double []));    } 
   int i,ibig,j;    nrerror("Too many iterations in brent"); 
   double del,t,*pt,*ptt,*xit;    *xmin=x; 
   double fp,fptt;    return fx; 
   double *xits;  } 
   pt=vector(1,n);  
   ptt=vector(1,n);  /****************** mnbrak ***********************/
   xit=vector(1,n);  
   xits=vector(1,n);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   *fret=(*func)(p);              double (*func)(double)) 
   for (j=1;j<=n;j++) pt[j]=p[j];  { 
   for (*iter=1;;++(*iter)) {    double ulim,u,r,q, dum;
     fp=(*fret);    double fu; 
     ibig=0;   
     del=0.0;    *fa=(*func)(*ax); 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    *fb=(*func)(*bx); 
     for (i=1;i<=n;i++)    if (*fb > *fa) { 
       printf(" %d %.12f",i, p[i]);      SHFT(dum,*ax,*bx,dum) 
     printf("\n");        SHFT(dum,*fb,*fa,dum) 
     for (i=1;i<=n;i++) {        } 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    *cx=(*bx)+GOLD*(*bx-*ax); 
       fptt=(*fret);    *fc=(*func)(*cx); 
 #ifdef DEBUG    while (*fb > *fc) { 
       printf("fret=%lf \n",*fret);      r=(*bx-*ax)*(*fb-*fc); 
 #endif      q=(*bx-*cx)*(*fb-*fa); 
       printf("%d",i);fflush(stdout);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       linmin(p,xit,n,fret,func);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       if (fabs(fptt-(*fret)) > del) {      ulim=(*bx)+GLIMIT*(*cx-*bx); 
         del=fabs(fptt-(*fret));      if ((*bx-u)*(u-*cx) > 0.0) { 
         ibig=i;        fu=(*func)(u); 
       }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
 #ifdef DEBUG        fu=(*func)(u); 
       printf("%d %.12e",i,(*fret));        if (fu < *fc) { 
       for (j=1;j<=n;j++) {          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);            SHFT(*fb,*fc,fu,(*func)(u)) 
         printf(" x(%d)=%.12e",j,xit[j]);            } 
       }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       for(j=1;j<=n;j++)        u=ulim; 
         printf(" p=%.12e",p[j]);        fu=(*func)(u); 
       printf("\n");      } else { 
 #endif        u=(*cx)+GOLD*(*cx-*bx); 
     }        fu=(*func)(u); 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      } 
 #ifdef DEBUG      SHFT(*ax,*bx,*cx,u) 
       int k[2],l;        SHFT(*fa,*fb,*fc,fu) 
       k[0]=1;        } 
       k[1]=-1;  } 
       printf("Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++)  /*************** linmin ************************/
         printf(" %.12e",p[j]);  
       printf("\n");  int ncom; 
       for(l=0;l<=1;l++) {  double *pcom,*xicom;
         for (j=1;j<=n;j++) {  double (*nrfunc)(double []); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];   
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         }  { 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    double brent(double ax, double bx, double cx, 
       }                 double (*f)(double), double tol, double *xmin); 
 #endif    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
       free_vector(xit,1,n);    int j; 
       free_vector(xits,1,n);    double xx,xmin,bx,ax; 
       free_vector(ptt,1,n);    double fx,fb,fa;
       free_vector(pt,1,n);   
       return;    ncom=n; 
     }    pcom=vector(1,n); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    xicom=vector(1,n); 
     for (j=1;j<=n;j++) {    nrfunc=func; 
       ptt[j]=2.0*p[j]-pt[j];    for (j=1;j<=n;j++) { 
       xit[j]=p[j]-pt[j];      pcom[j]=p[j]; 
       pt[j]=p[j];      xicom[j]=xi[j]; 
     }    } 
     fptt=(*func)(ptt);    ax=0.0; 
     if (fptt < fp) {    xx=1.0; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       if (t < 0.0) {    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
         linmin(p,xit,n,fret,func);  #ifdef DEBUG
         for (j=1;j<=n;j++) {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
           xi[j][ibig]=xi[j][n];    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
           xi[j][n]=xit[j];  #endif
         }    for (j=1;j<=n;j++) { 
 #ifdef DEBUG      xi[j] *= xmin; 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      p[j] += xi[j]; 
         for(j=1;j<=n;j++)    } 
           printf(" %.12e",xit[j]);    free_vector(xicom,1,n); 
         printf("\n");    free_vector(pcom,1,n); 
 #endif  } 
       }  
     }  /*************** powell ************************/
   }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 }              double (*func)(double [])) 
   { 
 /**** Prevalence limit ****************/    void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    int i,ibig,j; 
 {    double del,t,*pt,*ptt,*xit;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    double fp,fptt;
      matrix by transitions matrix until convergence is reached */    double *xits;
     pt=vector(1,n); 
   int i, ii,j,k;    ptt=vector(1,n); 
   double min, max, maxmin, maxmax,sumnew=0.;    xit=vector(1,n); 
   double **matprod2();    xits=vector(1,n); 
   double **out, cov[NCOVMAX], **pmij();    *fret=(*func)(p); 
   double **newm;    for (j=1;j<=n;j++) pt[j]=p[j]; 
   double agefin, delaymax=50 ; /* Max number of years to converge */    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
   for (ii=1;ii<=nlstate+ndeath;ii++)      ibig=0; 
     for (j=1;j<=nlstate+ndeath;j++){      del=0.0; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       for (i=1;i<=n;i++) 
    cov[1]=1.;        printf(" %d %.12f",i, p[i]);
        fprintf(ficlog," %d %.12f",i, p[i]);
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      printf("\n");
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      fprintf(ficlog,"\n");
     newm=savm;      for (i=1;i<=n;i++) { 
     /* Covariates have to be included here again */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
      cov[2]=agefin;        fptt=(*fret); 
    #ifdef DEBUG
       for (k=1; k<=cptcovn;k++) {        printf("fret=%lf \n",*fret);
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        fprintf(ficlog,"fret=%lf \n",*fret);
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  #endif
       }        printf("%d",i);fflush(stdout);
       for (k=1; k<=cptcovage;k++)        fprintf(ficlog,"%d",i);fflush(ficlog);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        linmin(p,xit,n,fret,func); 
       for (k=1; k<=cptcovprod;k++)        if (fabs(fptt-(*fret)) > del) { 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          del=fabs(fptt-(*fret)); 
           ibig=i; 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        } 
   #ifdef DEBUG
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"%d %.12e",i,(*fret));
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);        for (j=1;j<=n;j++) {
           xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     savm=oldm;          printf(" x(%d)=%.12e",j,xit[j]);
     oldm=newm;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     maxmax=0.;        }
     for(j=1;j<=nlstate;j++){        for(j=1;j<=n;j++) {
       min=1.;          printf(" p=%.12e",p[j]);
       max=0.;          fprintf(ficlog," p=%.12e",p[j]);
       for(i=1; i<=nlstate; i++) {        }
         sumnew=0;        printf("\n");
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        fprintf(ficlog,"\n");
         prlim[i][j]= newm[i][j]/(1-sumnew);  #endif
         max=FMAX(max,prlim[i][j]);      } 
         min=FMIN(min,prlim[i][j]);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       }  #ifdef DEBUG
       maxmin=max-min;        int k[2],l;
       maxmax=FMAX(maxmax,maxmin);        k[0]=1;
     }        k[1]=-1;
     if(maxmax < ftolpl){        printf("Max: %.12e",(*func)(p));
       return prlim;        fprintf(ficlog,"Max: %.12e",(*func)(p));
     }        for (j=1;j<=n;j++) {
   }          printf(" %.12e",p[j]);
 }          fprintf(ficlog," %.12e",p[j]);
         }
 /*************** transition probabilities **********/        printf("\n");
         fprintf(ficlog,"\n");
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        for(l=0;l<=1;l++) {
 {          for (j=1;j<=n;j++) {
   double s1, s2;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   /*double t34;*/            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   int i,j,j1, nc, ii, jj;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
     for(i=1; i<= nlstate; i++){          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for(j=1; j<i;j++){          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        }
         /*s2 += param[i][j][nc]*cov[nc];*/  #endif
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }        free_vector(xit,1,n); 
       ps[i][j]=s2;        free_vector(xits,1,n); 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        free_vector(ptt,1,n); 
     }        free_vector(pt,1,n); 
     for(j=i+1; j<=nlstate+ndeath;j++){        return; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      } 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      for (j=1;j<=n;j++) { 
       }        ptt[j]=2.0*p[j]-pt[j]; 
       ps[i][j]=s2;        xit[j]=p[j]-pt[j]; 
     }        pt[j]=p[j]; 
   }      } 
   for(i=1; i<= nlstate; i++){      fptt=(*func)(ptt); 
      s1=0;      if (fptt < fp) { 
     for(j=1; j<i; j++)        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       s1+=exp(ps[i][j]);        if (t < 0.0) { 
     for(j=i+1; j<=nlstate+ndeath; j++)          linmin(p,xit,n,fret,func); 
       s1+=exp(ps[i][j]);          for (j=1;j<=n;j++) { 
     ps[i][i]=1./(s1+1.);            xi[j][ibig]=xi[j][n]; 
     for(j=1; j<i; j++)            xi[j][n]=xit[j]; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];          }
     for(j=i+1; j<=nlstate+ndeath; j++)  #ifdef DEBUG
       ps[i][j]= exp(ps[i][j])*ps[i][i];          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   } /* end i */          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){            fprintf(ficlog," %.12e",xit[j]);
     for(jj=1; jj<= nlstate+ndeath; jj++){          }
       ps[ii][jj]=0;          printf("\n");
       ps[ii][ii]=1;          fprintf(ficlog,"\n");
     }  #endif
   }        }
       } 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    } 
     for(jj=1; jj<= nlstate+ndeath; jj++){  } 
      printf("%lf ",ps[ii][jj]);  
    }  /**** Prevalence limit (stable prevalence)  ****************/
     printf("\n ");  
     }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     printf("\n ");printf("%lf ",cov[2]);*/  {
 /*    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   for(i=1; i<= npar; i++) printf("%f ",x[i]);       matrix by transitions matrix until convergence is reached */
   goto end;*/  
     return ps;    int i, ii,j,k;
 }    double min, max, maxmin, maxmax,sumnew=0.;
     double **matprod2();
 /**************** Product of 2 matrices ******************/    double **out, cov[NCOVMAX], **pmij();
     double **newm;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    double agefin, delaymax=50 ; /* Max number of years to converge */
 {  
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    for (ii=1;ii<=nlstate+ndeath;ii++)
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      for (j=1;j<=nlstate+ndeath;j++){
   /* in, b, out are matrice of pointers which should have been initialized        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      before: only the contents of out is modified. The function returns      }
      a pointer to pointers identical to out */  
   long i, j, k;     cov[1]=1.;
   for(i=nrl; i<= nrh; i++)   
     for(k=ncolol; k<=ncoloh; k++)   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
         out[i][k] +=in[i][j]*b[j][k];      newm=savm;
       /* Covariates have to be included here again */
   return out;       cov[2]=agefin;
 }    
         for (k=1; k<=cptcovn;k++) {
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 /************* Higher Matrix Product ***************/          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
         }
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 {        for (k=1; k<=cptcovprod;k++)
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      duration (i.e. until  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
      (typically every 2 years instead of every month which is too big).        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
      Model is determined by parameters x and covariates have to be      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
      included manually here.  
       savm=oldm;
      */      oldm=newm;
       maxmax=0.;
   int i, j, d, h, k;      for(j=1;j<=nlstate;j++){
   double **out, cov[NCOVMAX];        min=1.;
   double **newm;        max=0.;
         for(i=1; i<=nlstate; i++) {
   /* Hstepm could be zero and should return the unit matrix */          sumnew=0;
   for (i=1;i<=nlstate+ndeath;i++)          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     for (j=1;j<=nlstate+ndeath;j++){          prlim[i][j]= newm[i][j]/(1-sumnew);
       oldm[i][j]=(i==j ? 1.0 : 0.0);          max=FMAX(max,prlim[i][j]);
       po[i][j][0]=(i==j ? 1.0 : 0.0);          min=FMIN(min,prlim[i][j]);
     }        }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        maxmin=max-min;
   for(h=1; h <=nhstepm; h++){        maxmax=FMAX(maxmax,maxmin);
     for(d=1; d <=hstepm; d++){      }
       newm=savm;      if(maxmax < ftolpl){
       /* Covariates have to be included here again */        return prlim;
       cov[1]=1.;      }
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    }
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  }
 for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /*************** transition probabilities ***************/ 
    for (k=1; k<=cptcovprod;k++)  
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
     double s1, s2;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    /*double t34;*/
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    int i,j,j1, nc, ii, jj;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      for(i=1; i<= nlstate; i++){
       savm=oldm;      for(j=1; j<i;j++){
       oldm=newm;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     }          /*s2 += param[i][j][nc]*cov[nc];*/
     for(i=1; i<=nlstate+ndeath; i++)          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       for(j=1;j<=nlstate+ndeath;j++) {          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         po[i][j][h]=newm[i][j];        }
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        ps[i][j]=s2;
          */        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       }      }
   } /* end h */      for(j=i+1; j<=nlstate+ndeath;j++){
   return po;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 }          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
         }
 /*************** log-likelihood *************/        ps[i][j]=s2;
 double func( double *x)      }
 {    }
   int i, ii, j, k, mi, d, kk;      /*ps[3][2]=1;*/
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;    for(i=1; i<= nlstate; i++){
   double sw; /* Sum of weights */       s1=0;
   double lli; /* Individual log likelihood */      for(j=1; j<i; j++)
   long ipmx;        s1+=exp(ps[i][j]);
   /*extern weight */      for(j=i+1; j<=nlstate+ndeath; j++)
   /* We are differentiating ll according to initial status */        s1+=exp(ps[i][j]);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      ps[i][i]=1./(s1+1.);
   /*for(i=1;i<imx;i++)      for(j=1; j<i; j++)
 printf(" %d\n",s[4][i]);        ps[i][j]= exp(ps[i][j])*ps[i][i];
   */      for(j=i+1; j<=nlstate+ndeath; j++)
   cov[1]=1.;        ps[i][j]= exp(ps[i][j])*ps[i][i];
       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   for(k=1; k<=nlstate; k++) ll[k]=0.;    } /* end i */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
        for(mi=1; mi<= wav[i]-1; mi++){      for(jj=1; jj<= nlstate+ndeath; jj++){
       for (ii=1;ii<=nlstate+ndeath;ii++)        ps[ii][jj]=0;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        ps[ii][ii]=1;
             for(d=0; d<dh[mi][i]; d++){      }
               newm=savm;    }
               cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
               for (kk=1; kk<=cptcovage;kk++) {  
                  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
                  /*printf("%d %d",kk,Tage[kk]);*/      for(jj=1; jj<= nlstate+ndeath; jj++){
               }       printf("%lf ",ps[ii][jj]);
               /*cov[4]=covar[1][i]*cov[2];scanf("%d", i);*/     }
               /*cov[3]=pow(cov[2],2)/1000.;*/      printf("\n ");
       }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      printf("\n ");printf("%lf ",cov[2]);*/
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  /*
           savm=oldm;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
           oldm=newm;    goto end;*/
       return ps;
   }
       } /* end mult */  
      /**************** Product of 2 matrices ******************/
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       ipmx +=1;  {
       sw += weight[i];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     } /* end of wave */    /* in, b, out are matrice of pointers which should have been initialized 
   } /* end of individual */       before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    long i, j, k;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    for(i=nrl; i<= nrh; i++)
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      for(k=ncolol; k<=ncoloh; k++)
   return -l;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
 }          out[i][k] +=in[i][j]*b[j][k];
   
     return out;
 /*********** Maximum Likelihood Estimation ***************/  }
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {  /************* Higher Matrix Product ***************/
   int i,j, iter;  
   double **xi,*delti;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   double fret;  {
   xi=matrix(1,npar,1,npar);    /* Computes the transition matrix starting at age 'age' over 
   for (i=1;i<=npar;i++)       'nhstepm*hstepm*stepm' months (i.e. until
     for (j=1;j<=npar;j++)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       xi[i][j]=(i==j ? 1.0 : 0.0);       nhstepm*hstepm matrices. 
   printf("Powell\n");       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   powell(p,xi,npar,ftol,&iter,&fret,func);       (typically every 2 years instead of every month which is too big 
        for the memory).
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));       Model is determined by parameters x and covariates have to be 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));       included manually here. 
   
 }       */
   
 /**** Computes Hessian and covariance matrix ***/    int i, j, d, h, k;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    double **out, cov[NCOVMAX];
 {    double **newm;
   double  **a,**y,*x,pd;  
   double **hess;    /* Hstepm could be zero and should return the unit matrix */
   int i, j,jk;    for (i=1;i<=nlstate+ndeath;i++)
   int *indx;      for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
   double hessii(double p[], double delta, int theta, double delti[]);        po[i][j][0]=(i==j ? 1.0 : 0.0);
   double hessij(double p[], double delti[], int i, int j);      }
   void lubksb(double **a, int npar, int *indx, double b[]) ;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   void ludcmp(double **a, int npar, int *indx, double *d) ;    for(h=1; h <=nhstepm; h++){
       for(d=1; d <=hstepm; d++){
         newm=savm;
   hess=matrix(1,npar,1,npar);        /* Covariates have to be included here again */
         cov[1]=1.;
   printf("\nCalculation of the hessian matrix. Wait...\n");        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   for (i=1;i<=npar;i++){        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     printf("%d",i);fflush(stdout);        for (k=1; k<=cptcovage;k++)
     hess[i][i]=hessii(p,ftolhess,i,delti);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     /*printf(" %f ",p[i]);*/        for (k=1; k<=cptcovprod;k++)
   }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++)  {        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       if (j>i) {        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         printf(".%d%d",i,j);fflush(stdout);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         hess[i][j]=hessij(p,delti,i,j);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         hess[j][i]=hess[i][j];        savm=oldm;
       }        oldm=newm;
     }      }
   }      for(i=1; i<=nlstate+ndeath; i++)
   printf("\n");        for(j=1;j<=nlstate+ndeath;j++) {
           po[i][j][h]=newm[i][j];
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
             */
   a=matrix(1,npar,1,npar);        }
   y=matrix(1,npar,1,npar);    } /* end h */
   x=vector(1,npar);    return po;
   indx=ivector(1,npar);  }
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  
   ludcmp(a,npar,indx,&pd);  /*************** log-likelihood *************/
   double func( double *x)
   for (j=1;j<=npar;j++) {  {
     for (i=1;i<=npar;i++) x[i]=0;    int i, ii, j, k, mi, d, kk;
     x[j]=1;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     lubksb(a,npar,indx,x);    double **out;
     for (i=1;i<=npar;i++){    double sw; /* Sum of weights */
       matcov[i][j]=x[i];    double lli; /* Individual log likelihood */
     }    int s1, s2;
   }    double bbh, survp;
     long ipmx;
   printf("\n#Hessian matrix#\n");    /*extern weight */
   for (i=1;i<=npar;i++) {    /* We are differentiating ll according to initial status */
     for (j=1;j<=npar;j++) {    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       printf("%.3e ",hess[i][j]);    /*for(i=1;i<imx;i++) 
     }      printf(" %d\n",s[4][i]);
     printf("\n");    */
   }    cov[1]=1.;
   
   /* Recompute Inverse */    for(k=1; k<=nlstate; k++) ll[k]=0.;
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    if(mle==1){
   ludcmp(a,npar,indx,&pd);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   /*  printf("\n#Hessian matrix recomputed#\n");        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   for (j=1;j<=npar;j++) {            for (j=1;j<=nlstate+ndeath;j++){
     for (i=1;i<=npar;i++) x[i]=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     x[j]=1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     lubksb(a,npar,indx,x);            }
     for (i=1;i<=npar;i++){          for(d=0; d<dh[mi][i]; d++){
       y[i][j]=x[i];            newm=savm;
       printf("%.3e ",y[i][j]);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     }            for (kk=1; kk<=cptcovage;kk++) {
     printf("\n");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
   */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_matrix(a,1,npar,1,npar);            savm=oldm;
   free_matrix(y,1,npar,1,npar);            oldm=newm;
   free_vector(x,1,npar);          } /* end mult */
   free_ivector(indx,1,npar);        
   free_matrix(hess,1,npar,1,npar);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias and large stepm.
            * If stepm is larger than one month (smallest stepm) and if the exact delay 
 }           * (in months) between two waves is not a multiple of stepm, we rounded to 
            * the nearest (and in case of equal distance, to the lowest) interval but now
 /*************** hessian matrix ****************/           * we keep into memory the bias bh[mi][i] and also the previous matrix product
 double hessii( double x[], double delta, int theta, double delti[])           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
 {           * probability in order to take into account the bias as a fraction of the way
   int i;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   int l=1, lmax=20;           * -stepm/2 to stepm/2 .
   double k1,k2;           * For stepm=1 the results are the same as for previous versions of Imach.
   double p2[NPARMAX+1];           * For stepm > 1 the results are less biased than in previous versions. 
   double res;           */
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          s1=s[mw[mi][i]][i];
   double fx;          s2=s[mw[mi+1][i]][i];
   int k=0,kmax=10;          bbh=(double)bh[mi][i]/(double)stepm; 
   double l1;          /* bias is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
   fx=func(x);           */
   for (i=1;i<=npar;i++) p2[i]=x[i];          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   for(l=0 ; l <=lmax; l++){          if( s2 > nlstate){ 
     l1=pow(10,l);            /* i.e. if s2 is a death state and if the date of death is known then the contribution
     delts=delt;               to the likelihood is the probability to die between last step unit time and current 
     for(k=1 ; k <kmax; k=k+1){               step unit time, which is also the differences between probability to die before dh 
       delt = delta*(l1*k);               and probability to die before dh-stepm . 
       p2[theta]=x[theta] +delt;               In version up to 0.92 likelihood was computed
       k1=func(p2)-fx;          as if date of death was unknown. Death was treated as any other
       p2[theta]=x[theta]-delt;          health state: the date of the interview describes the actual state
       k2=func(p2)-fx;          and not the date of a change in health state. The former idea was
       /*res= (k1-2.0*fx+k2)/delt/delt; */          to consider that at each interview the state was recorded
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          (healthy, disable or death) and IMaCh was corrected; but when we
                introduced the exact date of death then we should have modified
 #ifdef DEBUG          the contribution of an exact death to the likelihood. This new
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);          contribution is smaller and very dependent of the step unit
 #endif          stepm. It is no more the probability to die between last interview
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          and month of death but the probability to survive from last
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          interview up to one month before death multiplied by the
         k=kmax;          probability to die within a month. Thanks to Chris
       }          Jackson for correcting this bug.  Former versions increased
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          mortality artificially. The bad side is that we add another loop
         k=kmax; l=lmax*10.;          which slows down the processing. The difference can be up to 10%
       }          lower mortality.
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){            */
         delts=delt;            lli=log(out[s1][s2] - savm[s1][s2]);
       }          }else{
     }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   delti[theta]=delts;          } 
   return res;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
            /*if(lli ==000.0)*/
 }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
           ipmx +=1;
 double hessij( double x[], double delti[], int thetai,int thetaj)          sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int i;        } /* end of wave */
   int l=1, l1, lmax=20;      } /* end of individual */
   double k1,k2,k3,k4,res,fx;    }  else if(mle==2){
   double p2[NPARMAX+1];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int k;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   fx=func(x);          for (ii=1;ii<=nlstate+ndeath;ii++)
   for (k=1; k<=2; k++) {            for (j=1;j<=nlstate+ndeath;j++){
     for (i=1;i<=npar;i++) p2[i]=x[i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetai]=x[thetai]+delti[thetai]/k;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            }
     k1=func(p2)-fx;          for(d=0; d<=dh[mi][i]; d++){
              newm=savm;
     p2[thetai]=x[thetai]+delti[thetai]/k;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            for (kk=1; kk<=cptcovage;kk++) {
     k2=func(p2)-fx;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
     p2[thetai]=x[thetai]-delti[thetai]/k;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     k3=func(p2)-fx;            savm=oldm;
              oldm=newm;
     p2[thetai]=x[thetai]-delti[thetai]/k;          } /* end mult */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        
     k4=func(p2)-fx;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          /* But now since version 0.9 we anticipate for bias and large stepm.
 #ifdef DEBUG           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);           * (in months) between two waves is not a multiple of stepm, we rounded to 
 #endif           * the nearest (and in case of equal distance, to the lowest) interval but now
   }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   return res;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
 }           * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
 /************** Inverse of matrix **************/           * -stepm/2 to stepm/2 .
 void ludcmp(double **a, int n, int *indx, double *d)           * For stepm=1 the results are the same as for previous versions of Imach.
 {           * For stepm > 1 the results are less biased than in previous versions. 
   int i,imax,j,k;           */
   double big,dum,sum,temp;          s1=s[mw[mi][i]][i];
   double *vv;          s2=s[mw[mi+1][i]][i];
            bbh=(double)bh[mi][i]/(double)stepm; 
   vv=vector(1,n);          /* bias is positive if real duration
   *d=1.0;           * is higher than the multiple of stepm and negative otherwise.
   for (i=1;i<=n;i++) {           */
     big=0.0;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     for (j=1;j<=n;j++)          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       if ((temp=fabs(a[i][j])) > big) big=temp;          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     vv[i]=1.0/big;          /*if(lli ==000.0)*/
   }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   for (j=1;j<=n;j++) {          ipmx +=1;
     for (i=1;i<j;i++) {          sw += weight[i];
       sum=a[i][j];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        } /* end of wave */
       a[i][j]=sum;      } /* end of individual */
     }    }  else if(mle==3){  /* exponential inter-extrapolation */
     big=0.0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (i=j;i<=n;i++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       sum=a[i][j];        for(mi=1; mi<= wav[i]-1; mi++){
       for (k=1;k<j;k++)          for (ii=1;ii<=nlstate+ndeath;ii++)
         sum -= a[i][k]*a[k][j];            for (j=1;j<=nlstate+ndeath;j++){
       a[i][j]=sum;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       if ( (dum=vv[i]*fabs(sum)) >= big) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         big=dum;            }
         imax=i;          for(d=0; d<dh[mi][i]; d++){
       }            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     if (j != imax) {            for (kk=1; kk<=cptcovage;kk++) {
       for (k=1;k<=n;k++) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         dum=a[imax][k];            }
         a[imax][k]=a[j][k];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         a[j][k]=dum;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
       *d = -(*d);            oldm=newm;
       vv[imax]=vv[j];          } /* end mult */
     }        
     indx[j]=imax;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     if (a[j][j] == 0.0) a[j][j]=TINY;          /* But now since version 0.9 we anticipate for bias and large stepm.
     if (j != n) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       dum=1.0/(a[j][j]);           * (in months) between two waves is not a multiple of stepm, we rounded to 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;           * the nearest (and in case of equal distance, to the lowest) interval but now
     }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   }           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   free_vector(vv,1,n);  /* Doesn't work */           * probability in order to take into account the bias as a fraction of the way
 ;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
 }           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
 void lubksb(double **a, int n, int *indx, double b[])           * For stepm > 1 the results are less biased than in previous versions. 
 {           */
   int i,ii=0,ip,j;          s1=s[mw[mi][i]][i];
   double sum;          s2=s[mw[mi+1][i]][i];
            bbh=(double)bh[mi][i]/(double)stepm; 
   for (i=1;i<=n;i++) {          /* bias is positive if real duration
     ip=indx[i];           * is higher than the multiple of stepm and negative otherwise.
     sum=b[ip];           */
     b[ip]=b[i];          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
     if (ii)          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     else if (sum) ii=i;          /*if(lli ==000.0)*/
     b[i]=sum;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   }          ipmx +=1;
   for (i=n;i>=1;i--) {          sw += weight[i];
     sum=b[i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        } /* end of wave */
     b[i]=sum/a[i][i];      } /* end of individual */
   }    }else{  /* ml=4 no inter-extrapolation */
 }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 /************ Frequencies ********************/        for(mi=1; mi<= wav[i]-1; mi++){
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)          for (ii=1;ii<=nlstate+ndeath;ii++)
 {  /* Some frequencies */            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double ***freq; /* Frequencies */            }
   double *pp;          for(d=0; d<dh[mi][i]; d++){
   double pos;            newm=savm;
   FILE *ficresp;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   char fileresp[FILENAMELENGTH];            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   pp=vector(1,nlstate);            }
           
   strcpy(fileresp,"p");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   strcat(fileresp,fileres);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   if((ficresp=fopen(fileresp,"w"))==NULL) {            savm=oldm;
     printf("Problem with prevalence resultfile: %s\n", fileresp);            oldm=newm;
     exit(0);          } /* end mult */
   }        
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   j1=0;          ipmx +=1;
           sw += weight[i];
   j=cptcoveff;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        } /* end of wave */
       } /* end of individual */
   for(k1=1; k1<=j;k1++){    } /* End of if */
    for(i1=1; i1<=ncodemax[k1];i1++){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
        j1++;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         for (i=-1; i<=nlstate+ndeath; i++)      return -l;
          for (jk=-1; jk<=nlstate+ndeath; jk++)    }
            for(m=agemin; m <= agemax+3; m++)  
              freq[i][jk][m]=0;  
          /*********** Maximum Likelihood Estimation ***************/
        for (i=1; i<=imx; i++) {  
          bool=1;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
          if  (cptcovn>0) {  {
            for (z1=1; z1<=cptcoveff; z1++)    int i,j, iter;
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) bool=0;    double **xi;
          }    double fret;
           if (bool==1) {    xi=matrix(1,npar,1,npar);
            for(m=firstpass; m<=lastpass-1; m++){    for (i=1;i<=npar;i++)
              if(agev[m][i]==0) agev[m][i]=agemax+1;      for (j=1;j<=npar;j++)
              if(agev[m][i]==1) agev[m][i]=agemax+2;        xi[i][j]=(i==j ? 1.0 : 0.0);
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    printf("Powell\n");  fprintf(ficlog,"Powell\n");
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    powell(p,xi,npar,ftol,&iter,&fret,func);
            }  
          }     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
        }    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         if  (cptcovn>0) {    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
          fprintf(ficresp, "\n#********** Variable ");  
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  }
        }  
        fprintf(ficresp, "**********\n#");  /**** Computes Hessian and covariance matrix ***/
        for(i=1; i<=nlstate;i++)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  {
        fprintf(ficresp, "\n");    double  **a,**y,*x,pd;
            double **hess;
   for(i=(int)agemin; i <= (int)agemax+3; i++){    int i, j,jk;
     if(i==(int)agemax+3)    int *indx;
       printf("Total");  
     else    double hessii(double p[], double delta, int theta, double delti[]);
       printf("Age %d", i);    double hessij(double p[], double delti[], int i, int j);
     for(jk=1; jk <=nlstate ; jk++){    void lubksb(double **a, int npar, int *indx, double b[]) ;
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    void ludcmp(double **a, int npar, int *indx, double *d) ;
         pp[jk] += freq[jk][m][i];  
     }    hess=matrix(1,npar,1,npar);
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pos=0; m <=0 ; m++)    printf("\nCalculation of the hessian matrix. Wait...\n");
         pos += freq[jk][m][i];    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       if(pp[jk]>=1.e-10)    for (i=1;i<=npar;i++){
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      printf("%d",i);fflush(stdout);
       else      fprintf(ficlog,"%d",i);fflush(ficlog);
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      hess[i][i]=hessii(p,ftolhess,i,delti);
     }      /*printf(" %f ",p[i]);*/
     for(jk=1; jk <=nlstate ; jk++){      /*printf(" %lf ",hess[i][i]);*/
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)    }
         pp[jk] += freq[jk][m][i];    
     }    for (i=1;i<=npar;i++) {
     for(jk=1,pos=0; jk <=nlstate ; jk++)      for (j=1;j<=npar;j++)  {
       pos += pp[jk];        if (j>i) { 
     for(jk=1; jk <=nlstate ; jk++){          printf(".%d%d",i,j);fflush(stdout);
       if(pos>=1.e-5)          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          hess[i][j]=hessij(p,delti,i,j);
       else          hess[j][i]=hess[i][j];    
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          /*printf(" %lf ",hess[i][j]);*/
       if( i <= (int) agemax){        }
         if(pos>=1.e-5)      }
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    }
       else    printf("\n");
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    fprintf(ficlog,"\n");
       }  
     }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     for(jk=-1; jk <=nlstate+ndeath; jk++)    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       for(m=-1; m <=nlstate+ndeath; m++)    
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    a=matrix(1,npar,1,npar);
     if(i <= (int) agemax)    y=matrix(1,npar,1,npar);
       fprintf(ficresp,"\n");    x=vector(1,npar);
     printf("\n");    indx=ivector(1,npar);
     }    for (i=1;i<=npar;i++)
     }      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
  }    ludcmp(a,npar,indx,&pd);
    
   fclose(ficresp);    for (j=1;j<=npar;j++) {
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      for (i=1;i<=npar;i++) x[i]=0;
   free_vector(pp,1,nlstate);      x[j]=1;
       lubksb(a,npar,indx,x);
 }  /* End of Freq */      for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
 /************* Waves Concatenation ***************/      }
     }
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  
 {    printf("\n#Hessian matrix#\n");
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    fprintf(ficlog,"\n#Hessian matrix#\n");
      Death is a valid wave (if date is known).    for (i=1;i<=npar;i++) { 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      for (j=1;j<=npar;j++) { 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        printf("%.3e ",hess[i][j]);
      and mw[mi+1][i]. dh depends on stepm.        fprintf(ficlog,"%.3e ",hess[i][j]);
      */      }
       printf("\n");
   int i, mi, m;      fprintf(ficlog,"\n");
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    }
 float sum=0.;  
     /* Recompute Inverse */
   for(i=1; i<=imx; i++){    for (i=1;i<=npar;i++)
     mi=0;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     m=firstpass;    ludcmp(a,npar,indx,&pd);
     while(s[m][i] <= nlstate){  
       if(s[m][i]>=1)    /*  printf("\n#Hessian matrix recomputed#\n");
         mw[++mi][i]=m;  
       if(m >=lastpass)    for (j=1;j<=npar;j++) {
         break;      for (i=1;i<=npar;i++) x[i]=0;
       else      x[j]=1;
         m++;      lubksb(a,npar,indx,x);
     }/* end while */      for (i=1;i<=npar;i++){ 
     if (s[m][i] > nlstate){        y[i][j]=x[i];
       mi++;     /* Death is another wave */        printf("%.3e ",y[i][j]);
       /* if(mi==0)  never been interviewed correctly before death */        fprintf(ficlog,"%.3e ",y[i][j]);
          /* Only death is a correct wave */      }
       mw[mi][i]=m;      printf("\n");
     }      fprintf(ficlog,"\n");
     }
     wav[i]=mi;    */
     if(mi==0)  
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    free_matrix(a,1,npar,1,npar);
   }    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
   for(i=1; i<=imx; i++){    free_ivector(indx,1,npar);
     for(mi=1; mi<wav[i];mi++){    free_matrix(hess,1,npar,1,npar);
       if (stepm <=0)  
         dh[mi][i]=1;  
       else{  }
         if (s[mw[mi+1][i]][i] > nlstate) {  
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  /*************** hessian matrix ****************/
           if(j=0) j=1;  /* Survives at least one month after exam */  double hessii( double x[], double delta, int theta, double delti[])
         }  {
         else{    int i;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    int l=1, lmax=20;
           k=k+1;    double k1,k2;
           if (j >= jmax) jmax=j;    double p2[NPARMAX+1];
           else if (j <= jmin)jmin=j;    double res;
           sum=sum+j;    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         }    double fx;
         jk= j/stepm;    int k=0,kmax=10;
         jl= j -jk*stepm;    double l1;
         ju= j -(jk+1)*stepm;  
         if(jl <= -ju)    fx=func(x);
           dh[mi][i]=jk;    for (i=1;i<=npar;i++) p2[i]=x[i];
         else    for(l=0 ; l <=lmax; l++){
           dh[mi][i]=jk+1;      l1=pow(10,l);
         if(dh[mi][i]==0)      delts=delt;
           dh[mi][i]=1; /* At least one step */      for(k=1 ; k <kmax; k=k+1){
       }        delt = delta*(l1*k);
     }        p2[theta]=x[theta] +delt;
   }        k1=func(p2)-fx;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);        p2[theta]=x[theta]-delt;
 }        k2=func(p2)-fx;
 /*********** Tricode ****************************/        /*res= (k1-2.0*fx+k2)/delt/delt; */
 void tricode(int *Tvar, int **nbcode, int imx)        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
 {        
   int Ndum[20],ij=1, k, j, i;  #ifdef DEBUG
   int cptcode=0;        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   cptcoveff=0;        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
    #endif
   for (k=0; k<19; k++) Ndum[k]=0;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   for (k=1; k<=7; k++) ncodemax[k]=0;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        }
     for (i=1; i<=imx; i++) {        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       ij=(int)(covar[Tvar[j]][i]);          k=kmax; l=lmax*10.;
       Ndum[ij]++;        }
       if (ij > cptcode) cptcode=ij;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     }          delts=delt;
         }
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/      }
     for (i=0; i<=cptcode; i++) {    }
       if(Ndum[i]!=0) ncodemax[j]++;    delti[theta]=delts;
     }    return res; 
     ij=1;    
   }
     for (i=1; i<=ncodemax[j]; i++) {  
       for (k=0; k<=19; k++) {  double hessij( double x[], double delti[], int thetai,int thetaj)
         if (Ndum[k] != 0) {  {
           nbcode[Tvar[j]][ij]=k;    int i;
           /*   printf("ij=%d ",nbcode[Tvar[2]][1]);*/    int l=1, l1, lmax=20;
           ij++;    double k1,k2,k3,k4,res,fx;
         }    double p2[NPARMAX+1];
         if (ij > ncodemax[j]) break;    int k;
       }    
     }    fx=func(x);
   }      for (k=1; k<=2; k++) {
  for (i=1; i<=10; i++) {      for (i=1;i<=npar;i++) p2[i]=x[i];
       ij=Tvar[i];      p2[thetai]=x[thetai]+delti[thetai]/k;
       Ndum[ij]++;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     }      k1=func(p2)-fx;
  ij=1;    
  for (i=1; i<=cptcovn; i++) {      p2[thetai]=x[thetai]+delti[thetai]/k;
    if((Ndum[i]!=0) && (i<=ncov)){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
      Tvaraff[i]=ij;      k2=func(p2)-fx;
    ij++;    
    }      p2[thetai]=x[thetai]-delti[thetai]/k;
  }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
        k3=func(p2)-fx;
  for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    
    if ((Tvar[j]>= cptcoveff) && (Tvar[j] <=ncov)) cptcoveff=Tvar[j];      p2[thetai]=x[thetai]-delti[thetai]/k;
    /*printf("j=%d %d\n",j,Tvar[j]);*/      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
  }      k4=func(p2)-fx;
        res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
  /* printf("cptcoveff=%d Tvaraff=%d %d\n",cptcoveff, Tvaraff[1],Tvaraff[2]);  #ifdef DEBUG
     scanf("%d",i);*/      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
 }      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   #endif
 /*********** Health Expectancies ****************/    }
     return res;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)  }
 {  
   /* Health expectancies */  /************** Inverse of matrix **************/
   int i, j, nhstepm, hstepm, h;  void ludcmp(double **a, int n, int *indx, double *d) 
   double age, agelim,hf;  { 
   double ***p3mat;    int i,imax,j,k; 
      double big,dum,sum,temp; 
   fprintf(ficreseij,"# Health expectancies\n");    double *vv; 
   fprintf(ficreseij,"# Age");   
   for(i=1; i<=nlstate;i++)    vv=vector(1,n); 
     for(j=1; j<=nlstate;j++)    *d=1.0; 
       fprintf(ficreseij," %1d-%1d",i,j);    for (i=1;i<=n;i++) { 
   fprintf(ficreseij,"\n");      big=0.0; 
       for (j=1;j<=n;j++) 
   hstepm=1*YEARM; /*  Every j years of age (in month) */        if ((temp=fabs(a[i][j])) > big) big=temp; 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
   agelim=AGESUP;    } 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    for (j=1;j<=n;j++) { 
     /* nhstepm age range expressed in number of stepm */      for (i=1;i<j;i++) { 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);        sum=a[i][j]; 
     /* Typically if 20 years = 20*12/6=40 stepm */        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     if (stepm >= YEARM) hstepm=1;        a[i][j]=sum; 
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */      } 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      big=0.0; 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      for (i=j;i<=n;i++) { 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        sum=a[i][j]; 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
     for(i=1; i<=nlstate;i++)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       for(j=1; j<=nlstate;j++)          big=dum; 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          imax=i; 
           eij[i][j][(int)age] +=p3mat[i][j][h];        } 
         }      } 
          if (j != imax) { 
     hf=1;        for (k=1;k<=n;k++) { 
     if (stepm >= YEARM) hf=stepm/YEARM;          dum=a[imax][k]; 
     fprintf(ficreseij,"%.0f",age );          a[imax][k]=a[j][k]; 
     for(i=1; i<=nlstate;i++)          a[j][k]=dum; 
       for(j=1; j<=nlstate;j++){        } 
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);        *d = -(*d); 
       }        vv[imax]=vv[j]; 
     fprintf(ficreseij,"\n");      } 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      indx[j]=imax; 
   }      if (a[j][j] == 0.0) a[j][j]=TINY; 
 }      if (j != n) { 
         dum=1.0/(a[j][j]); 
 /************ Variance ******************/        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)      } 
 {    } 
   /* Variance of health expectancies */    free_vector(vv,1,n);  /* Doesn't work */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  ;
   double **newm;  } 
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm, h;  void lubksb(double **a, int n, int *indx, double b[]) 
   int k, cptcode;  { 
    double *xp;    int i,ii=0,ip,j; 
   double **gp, **gm;    double sum; 
   double ***gradg, ***trgradg;   
   double ***p3mat;    for (i=1;i<=n;i++) { 
   double age,agelim;      ip=indx[i]; 
   int theta;      sum=b[ip]; 
       b[ip]=b[i]; 
    fprintf(ficresvij,"# Covariances of life expectancies\n");      if (ii) 
   fprintf(ficresvij,"# Age");        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   for(i=1; i<=nlstate;i++)      else if (sum) ii=i; 
     for(j=1; j<=nlstate;j++)      b[i]=sum; 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    } 
   fprintf(ficresvij,"\n");    for (i=n;i>=1;i--) { 
       sum=b[i]; 
   xp=vector(1,npar);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   dnewm=matrix(1,nlstate,1,npar);      b[i]=sum/a[i][i]; 
   doldm=matrix(1,nlstate,1,nlstate);    } 
    } 
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  /************ Frequencies ********************/
   agelim = AGESUP;  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  {  /* Some frequencies */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    
     if (stepm >= YEARM) hstepm=1;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    int first;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double ***freq; /* Frequencies */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    double *pp, **prop;
     gp=matrix(0,nhstepm,1,nlstate);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     gm=matrix(0,nhstepm,1,nlstate);    FILE *ficresp;
     char fileresp[FILENAMELENGTH];
     for(theta=1; theta <=npar; theta++){    
       for(i=1; i<=npar; i++){ /* Computes gradient */    pp=vector(1,nlstate);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    prop=matrix(1,nlstate,iagemin,iagemax+3);
       }    strcpy(fileresp,"p");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      strcat(fileresp,fileres);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    if((ficresp=fopen(fileresp,"w"))==NULL) {
       for(j=1; j<= nlstate; j++){      printf("Problem with prevalence resultfile: %s\n", fileresp);
         for(h=0; h<=nhstepm; h++){      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      exit(0);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    }
         }    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
       }    j1=0;
        
       for(i=1; i<=npar; i++) /* Computes gradient */    j=cptcoveff;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    first=1;
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){    for(k1=1; k1<=j;k1++){
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      for(i1=1; i1<=ncodemax[k1];i1++){
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        j1++;
         }        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       }          scanf("%d", i);*/
       for(j=1; j<= nlstate; j++)        for (i=-1; i<=nlstate+ndeath; i++)  
         for(h=0; h<=nhstepm; h++){          for (jk=-1; jk<=nlstate+ndeath; jk++)  
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            for(m=iagemin; m <= iagemax+3; m++)
         }              freq[i][jk][m]=0;
     } /* End theta */  
       for (i=1; i<=nlstate; i++)  
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
     for(h=0; h<=nhstepm; h++)        
       for(j=1; j<=nlstate;j++)        dateintsum=0;
         for(theta=1; theta <=npar; theta++)        k2cpt=0;
           trgradg[h][j][theta]=gradg[h][theta][j];        for (i=1; i<=imx; i++) {
           bool=1;
     for(i=1;i<=nlstate;i++)          if  (cptcovn>0) {
       for(j=1;j<=nlstate;j++)            for (z1=1; z1<=cptcoveff; z1++) 
         vareij[i][j][(int)age] =0.;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     for(h=0;h<=nhstepm;h++){                bool=0;
       for(k=0;k<=nhstepm;k++){          }
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          if (bool==1){
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            for(m=firstpass; m<=lastpass; m++){
         for(i=1;i<=nlstate;i++)              k2=anint[m][i]+(mint[m][i]/12.);
           for(j=1;j<=nlstate;j++)              if ((k2>=dateprev1) && (k2<=dateprev2)) {
             vareij[i][j][(int)age] += doldm[i][j];                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     }                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     h=1;                if (m<lastpass) {
     if (stepm >= YEARM) h=stepm/YEARM;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     fprintf(ficresvij,"%.0f ",age );                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     for(i=1; i<=nlstate;i++)                }
       for(j=1; j<=nlstate;j++){                
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
       }                  dateintsum=dateintsum+k2;
     fprintf(ficresvij,"\n");                  k2cpt++;
     free_matrix(gp,0,nhstepm,1,nlstate);                }
     free_matrix(gm,0,nhstepm,1,nlstate);              }
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            }
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
   } /* End age */         
          fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);        if  (cptcovn>0) {
   free_matrix(dnewm,1,nlstate,1,nlstate);          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 }          fprintf(ficresp, "**********\n#");
         }
 /************ Variance of prevlim ******************/        for(i=1; i<=nlstate;i++) 
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 {        fprintf(ficresp, "\n");
   /* Variance of prevalence limit */        
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        for(i=iagemin; i <= iagemax+3; i++){
   double **newm;          if(i==iagemax+3){
   double **dnewm,**doldm;            fprintf(ficlog,"Total");
   int i, j, nhstepm, hstepm;          }else{
   int k, cptcode;            if(first==1){
   double *xp;              first=0;
   double *gp, *gm;              printf("See log file for details...\n");
   double **gradg, **trgradg;            }
   double age,agelim;            fprintf(ficlog,"Age %d", i);
   int theta;          }
              for(jk=1; jk <=nlstate ; jk++){
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   fprintf(ficresvpl,"# Age");              pp[jk] += freq[jk][m][i]; 
   for(i=1; i<=nlstate;i++)          }
       fprintf(ficresvpl," %1d-%1d",i,i);          for(jk=1; jk <=nlstate ; jk++){
   fprintf(ficresvpl,"\n");            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
   xp=vector(1,npar);            if(pp[jk]>=1.e-10){
   dnewm=matrix(1,nlstate,1,npar);              if(first==1){
   doldm=matrix(1,nlstate,1,nlstate);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                }
   hstepm=1*YEARM; /* Every year of age */              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            }else{
   agelim = AGESUP;              if(first==1)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     if (stepm >= YEARM) hstepm=1;            }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          }
     gradg=matrix(1,npar,1,nlstate);  
     gp=vector(1,nlstate);          for(jk=1; jk <=nlstate ; jk++){
     gm=vector(1,nlstate);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
     for(theta=1; theta <=npar; theta++){          }       
       for(i=1; i<=npar; i++){ /* Computes gradient */          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            pos += pp[jk];
       }            posprop += prop[jk][i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          }
       for(i=1;i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
         gp[i] = prlim[i][i];            if(pos>=1.e-5){
                  if(first==1)
       for(i=1; i<=npar; i++) /* Computes gradient */                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            }else{
       for(i=1;i<=nlstate;i++)              if(first==1)
         gm[i] = prlim[i][i];                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       for(i=1;i<=nlstate;i++)            }
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];            if( i <= iagemax){
     } /* End theta */              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     trgradg =matrix(1,nlstate,1,npar);                probs[i][jk][j1]= pp[jk]/pos;
                 /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     for(j=1; j<=nlstate;j++)              }
       for(theta=1; theta <=npar; theta++)              else
         trgradg[j][theta]=gradg[theta][j];                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
     for(i=1;i<=nlstate;i++)          }
       varpl[i][(int)age] =0.;          
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          for(jk=-1; jk <=nlstate+ndeath; jk++)
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);            for(m=-1; m <=nlstate+ndeath; m++)
     for(i=1;i<=nlstate;i++)              if(freq[jk][m][i] !=0 ) {
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */              if(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     fprintf(ficresvpl,"%.0f ",age );                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     for(i=1; i<=nlstate;i++)              }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          if(i <= iagemax)
     fprintf(ficresvpl,"\n");            fprintf(ficresp,"\n");
     free_vector(gp,1,nlstate);          if(first==1)
     free_vector(gm,1,nlstate);            printf("Others in log...\n");
     free_matrix(gradg,1,npar,1,nlstate);          fprintf(ficlog,"\n");
     free_matrix(trgradg,1,nlstate,1,npar);        }
   } /* End age */      }
     }
   free_vector(xp,1,npar);    dateintmean=dateintsum/k2cpt; 
   free_matrix(doldm,1,nlstate,1,npar);   
   free_matrix(dnewm,1,nlstate,1,nlstate);    fclose(ficresp);
     free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
 }    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
   }
 /***********************************************/  
 /**************** Main Program *****************/  /************ Prevalence ********************/
 /***********************************************/  void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   {  
 /*int main(int argc, char *argv[])*/    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
 int main()       in each health status at the date of interview (if between dateprev1 and dateprev2).
 {       We still use firstpass and lastpass as another selection.
     */
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;   
   double agedeb, agefin,hf;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   double agemin=1.e20, agemax=-1.e20;    double ***freq; /* Frequencies */
     double *pp, **prop;
   double fret;    double pos,posprop; 
   double **xi,tmp,delta;    double  y2; /* in fractional years */
     int iagemin, iagemax;
   double dum; /* Dummy variable */  
   double ***p3mat;    iagemin= (int) agemin;
   int *indx;    iagemax= (int) agemax;
   char line[MAXLINE], linepar[MAXLINE];    /*pp=vector(1,nlstate);*/
   char title[MAXLINE];    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];    j1=0;
   char filerest[FILENAMELENGTH];    
   char fileregp[FILENAMELENGTH];    j=cptcoveff;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   int firstobs=1, lastobs=10;    
   int sdeb, sfin; /* Status at beginning and end */    for(k1=1; k1<=j;k1++){
   int c,  h , cpt,l;      for(i1=1; i1<=ncodemax[k1];i1++){
   int ju,jl, mi;        j1++;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        for (i=1; i<=nlstate; i++)  
            for(m=iagemin; m <= iagemax+3; m++)
   int hstepm, nhstepm;            prop[i][m]=0.0;
   double bage, fage, age, agelim, agebase;       
   double ftolpl=FTOL;        for (i=1; i<=imx; i++) { /* Each individual */
   double **prlim;          bool=1;
   double *severity;          if  (cptcovn>0) {
   double ***param; /* Matrix of parameters */            for (z1=1; z1<=cptcoveff; z1++) 
   double  *p;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   double **matcov; /* Matrix of covariance */                bool=0;
   double ***delti3; /* Scale */          } 
   double *delti; /* Scale */          if (bool==1) { 
   double ***eij, ***vareij;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   double **varpl; /* Variances of prevalence limits by age */              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   double *epj, vepp;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   char *alph[]={"a","a","b","c","d","e"}, str[4];                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   char z[1]="c", occ;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
 #include <sys/time.h>                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
 #include <time.h>                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];                  prop[s[m][i]][iagemax+3] += weight[i]; 
   /* long total_usecs;                } 
   struct timeval start_time, end_time;              }
              } /* end selection of waves */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          }
         }
         for(i=iagemin; i <= iagemax+3; i++){  
   printf("\nIMACH, Version 0.64a");          
   printf("\nEnter the parameter file name: ");          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
 #ifdef windows          } 
   scanf("%s",pathtot);  
   getcwd(pathcd, size);          for(jk=1; jk <=nlstate ; jk++){     
   /*cygwin_split_path(pathtot,path,optionfile);            if( i <=  iagemax){ 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/              if(posprop>=1.e-5){ 
   /* cutv(path,optionfile,pathtot,'\\');*/                probs[i][jk][j1]= prop[jk][i]/posprop;
               } 
 split(pathtot, path,optionfile);            } 
   chdir(path);          }/* end jk */ 
   replace(pathc,path);        }/* end i */ 
 #endif      } /* end i1 */
 #ifdef unix    } /* end k1 */
   scanf("%s",optionfile);    
 #endif    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
 /*-------- arguments in the command line --------*/    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
   strcpy(fileres,"r");  
   strcat(fileres, optionfile);  /************* Waves Concatenation ***************/
   
   /*---------arguments file --------*/  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
   {
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     printf("Problem with optionfile %s\n",optionfile);       Death is a valid wave (if date is known).
     goto end;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
   strcpy(filereso,"o");       */
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) {    int i, mi, m;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   }       double sum=0., jmean=0.;*/
     int first;
   /* Reads comments: lines beginning with '#' */    int j, k=0,jk, ju, jl;
   while((c=getc(ficpar))=='#' && c!= EOF){    double sum=0.;
     ungetc(c,ficpar);    first=0;
     fgets(line, MAXLINE, ficpar);    jmin=1e+5;
     puts(line);    jmax=-1;
     fputs(line,ficparo);    jmean=0.;
   }    for(i=1; i<=imx; i++){
   ungetc(c,ficpar);      mi=0;
       m=firstpass;
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);      while(s[m][i] <= nlstate){
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);        if(s[m][i]>=1)
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);          mw[++mi][i]=m;
         if(m >=lastpass)
   covar=matrix(0,NCOVMAX,1,n);              break;
   if (strlen(model)<=1) cptcovn=0;        else
   else {          m++;
     j=0;      }/* end while */
     j=nbocc(model,'+');      if (s[m][i] > nlstate){
     cptcovn=j+1;        mi++;     /* Death is another wave */
   }        /* if(mi==0)  never been interviewed correctly before death */
            /* Only death is a correct wave */
   ncovmodel=2+cptcovn;        mw[mi][i]=m;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      }
    
   /* Read guess parameters */      wav[i]=mi;
   /* Reads comments: lines beginning with '#' */      if(mi==0){
   while((c=getc(ficpar))=='#' && c!= EOF){        if(first==0){
     ungetc(c,ficpar);          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
     fgets(line, MAXLINE, ficpar);          first=1;
     puts(line);        }
     fputs(line,ficparo);        if(first==1){
   }          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
   ungetc(c,ficpar);        }
        } /* end mi==0 */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    }
     for(i=1; i <=nlstate; i++)  
     for(j=1; j <=nlstate+ndeath-1; j++){    for(i=1; i<=imx; i++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);      for(mi=1; mi<wav[i];mi++){
       fprintf(ficparo,"%1d%1d",i1,j1);        if (stepm <=0)
       printf("%1d%1d",i,j);          dh[mi][i]=1;
       for(k=1; k<=ncovmodel;k++){        else{
         fscanf(ficpar," %lf",&param[i][j][k]);          if (s[mw[mi+1][i]][i] > nlstate) {
         printf(" %lf",param[i][j][k]);            if (agedc[i] < 2*AGESUP) {
         fprintf(ficparo," %lf",param[i][j][k]);            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       }            if(j==0) j=1;  /* Survives at least one month after exam */
       fscanf(ficpar,"\n");            k=k+1;
       printf("\n");            if (j >= jmax) jmax=j;
       fprintf(ficparo,"\n");            if (j <= jmin) jmin=j;
     }            sum=sum+j;
              /*if (j<0) printf("j=%d num=%d \n",j,i); */
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   p=param[1][1];            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
              }
   /* Reads comments: lines beginning with '#' */          }
   while((c=getc(ficpar))=='#' && c!= EOF){          else{
     ungetc(c,ficpar);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     fgets(line, MAXLINE, ficpar);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     puts(line);            k=k+1;
     fputs(line,ficparo);            if (j >= jmax) jmax=j;
   }            else if (j <= jmin)jmin=j;
   ungetc(c,ficpar);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            sum=sum+j;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          }
   for(i=1; i <=nlstate; i++){          jk= j/stepm;
     for(j=1; j <=nlstate+ndeath-1; j++){          jl= j -jk*stepm;
       fscanf(ficpar,"%1d%1d",&i1,&j1);          ju= j -(jk+1)*stepm;
       printf("%1d%1d",i,j);          if(mle <=1){ 
       fprintf(ficparo,"%1d%1d",i1,j1);            if(jl==0){
       for(k=1; k<=ncovmodel;k++){              dh[mi][i]=jk;
         fscanf(ficpar,"%le",&delti3[i][j][k]);              bh[mi][i]=0;
         printf(" %le",delti3[i][j][k]);            }else{ /* We want a negative bias in order to only have interpolation ie
         fprintf(ficparo," %le",delti3[i][j][k]);                    * at the price of an extra matrix product in likelihood */
       }              dh[mi][i]=jk+1;
       fscanf(ficpar,"\n");              bh[mi][i]=ju;
       printf("\n");            }
       fprintf(ficparo,"\n");          }else{
     }            if(jl <= -ju){
   }              dh[mi][i]=jk;
   delti=delti3[1][1];              bh[mi][i]=jl;       /* bias is positive if real duration
                                     * is higher than the multiple of stepm and negative otherwise.
   /* Reads comments: lines beginning with '#' */                                   */
   while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);            else{
     fgets(line, MAXLINE, ficpar);              dh[mi][i]=jk+1;
     puts(line);              bh[mi][i]=ju;
     fputs(line,ficparo);            }
   }            if(dh[mi][i]==0){
   ungetc(c,ficpar);              dh[mi][i]=1; /* At least one step */
                bh[mi][i]=ju; /* At least one step */
   matcov=matrix(1,npar,1,npar);              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
   for(i=1; i <=npar; i++){            }
     fscanf(ficpar,"%s",&str);          }
     printf("%s",str);        } /* end if mle */
     fprintf(ficparo,"%s",str);      } /* end wave */
     for(j=1; j <=i; j++){    }
       fscanf(ficpar," %le",&matcov[i][j]);    jmean=sum/k;
       printf(" %.5le",matcov[i][j]);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       fprintf(ficparo," %.5le",matcov[i][j]);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     }   }
     fscanf(ficpar,"\n");  
     printf("\n");  /*********** Tricode ****************************/
     fprintf(ficparo,"\n");  void tricode(int *Tvar, int **nbcode, int imx)
   }  {
   for(i=1; i <=npar; i++)    
     for(j=i+1;j<=npar;j++)    int Ndum[20],ij=1, k, j, i, maxncov=19;
       matcov[i][j]=matcov[j][i];    int cptcode=0;
        cptcoveff=0; 
   printf("\n");   
     for (k=0; k<maxncov; k++) Ndum[k]=0;
     for (k=1; k<=7; k++) ncodemax[k]=0;
     /*-------- data file ----------*/  
     if((ficres =fopen(fileres,"w"))==NULL) {    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       printf("Problem with resultfile: %s\n", fileres);goto end;      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     }                                 modality*/ 
     fprintf(ficres,"#%s\n",version);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
            Ndum[ij]++; /*store the modality */
     if((fic=fopen(datafile,"r"))==NULL)    {        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       printf("Problem with datafile: %s\n", datafile);goto end;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     }                                         Tvar[j]. If V=sex and male is 0 and 
                                          female is 1, then  cptcode=1.*/
     n= lastobs;      }
     severity = vector(1,maxwav);  
     outcome=imatrix(1,maxwav+1,1,n);      for (i=0; i<=cptcode; i++) {
     num=ivector(1,n);        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
     moisnais=vector(1,n);      }
     annais=vector(1,n);  
     moisdc=vector(1,n);      ij=1; 
     andc=vector(1,n);      for (i=1; i<=ncodemax[j]; i++) {
     agedc=vector(1,n);        for (k=0; k<= maxncov; k++) {
     cod=ivector(1,n);          if (Ndum[k] != 0) {
     weight=vector(1,n);            nbcode[Tvar[j]][ij]=k; 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     mint=matrix(1,maxwav,1,n);            
     anint=matrix(1,maxwav,1,n);            ij++;
     s=imatrix(1,maxwav+1,1,n);          }
     adl=imatrix(1,maxwav+1,1,n);              if (ij > ncodemax[j]) break; 
     tab=ivector(1,NCOVMAX);        }  
     ncodemax=ivector(1,8);      } 
     }  
     i=1;  
     while (fgets(line, MAXLINE, fic) != NULL)    {   for (k=0; k< maxncov; k++) Ndum[k]=0;
       if ((i >= firstobs) && (i <=lastobs)) {  
           for (i=1; i<=ncovmodel-2; i++) { 
         for (j=maxwav;j>=1;j--){     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);     ij=Tvar[i];
           strcpy(line,stra);     Ndum[ij]++;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);   }
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }   ij=1;
           for (i=1; i<= maxncov; i++) {
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);     if((Ndum[i]!=0) && (i<=ncovcol)){
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);       Tvaraff[ij]=i; /*For printing */
        ij++;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);     }
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);   }
    
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);   cptcoveff=ij-1; /*Number of simple covariates*/
         for (j=ncov;j>=1;j--){  }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }  /*********** Health Expectancies ****************/
         num[i]=atol(stra);  
   void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
         /*printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/  
   {
         i=i+1;    /* Health expectancies */
       }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     }    double age, agelim, hf;
     double ***p3mat,***varhe;
     /*scanf("%d",i);*/    double **dnewm,**doldm;
   imx=i-1; /* Number of individuals */    double *xp;
     double **gp, **gm;
   /* Calculation of the number of parameter from char model*/    double ***gradg, ***trgradg;
   Tvar=ivector(1,15);    int theta;
   Tprod=ivector(1,15);  
   Tvaraff=ivector(1,15);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   Tvard=imatrix(1,15,1,2);    xp=vector(1,npar);
   Tage=ivector(1,15);          dnewm=matrix(1,nlstate*nlstate,1,npar);
        doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   if (strlen(model) >1){    
     j=0, j1=0, k1=1, k2=1;    fprintf(ficreseij,"# Health expectancies\n");
     j=nbocc(model,'+');    fprintf(ficreseij,"# Age");
     j1=nbocc(model,'*');    for(i=1; i<=nlstate;i++)
     cptcovn=j+1;      for(j=1; j<=nlstate;j++)
     cptcovprod=j1;        fprintf(ficreseij," %1d-%1d (SE)",i,j);
        fprintf(ficreseij,"\n");
     strcpy(modelsav,model);  
    if (j==0) {    if(estepm < stepm){
       if (j1==0){      printf ("Problem %d lower than %d\n",estepm, stepm);
         cutv(stra,strb,modelsav,'V');    }
         Tvar[1]=atoi(strb);    else  hstepm=estepm;   
       }    /* We compute the life expectancy from trapezoids spaced every estepm months
       else if (j1==1) {     * This is mainly to measure the difference between two models: for example
         cutv(stra,strb,modelsav,'*');     * if stepm=24 months pijx are given only every 2 years and by summing them
         Tage[1]=1; cptcovage++;     * we are calculating an estimate of the Life Expectancy assuming a linear 
         if (strcmp(stra,"age")==0) {     * progression in between and thus overestimating or underestimating according
           cptcovprod--;     * to the curvature of the survival function. If, for the same date, we 
           cutv(strd,strc,strb,'V');     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           Tvar[1]=atoi(strc);     * to compare the new estimate of Life expectancy with the same linear 
         }     * hypothesis. A more precise result, taking into account a more precise
         else if (strcmp(strb,"age")==0) {     * curvature will be obtained if estepm is as small as stepm. */
           cptcovprod--;  
           cutv(strd,strc,stra,'V');    /* For example we decided to compute the life expectancy with the smallest unit */
           Tvar[1]=atoi(strc);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         }       nhstepm is the number of hstepm from age to agelim 
         else {       nstepm is the number of stepm from age to agelin. 
           cutv(strd,strc,strb,'V');       Look at hpijx to understand the reason of that which relies in memory size
           cutv(stre,strd,stra,'V');       and note for a fixed period like estepm months */
           Tvar[1]=ncov+1;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           for (k=1; k<=lastobs;k++)       survival function given by stepm (the optimization length). Unfortunately it
               covar[ncov+1][k]=covar[atoi(strc)][k]*covar[atoi(strd)][k];       means that if the survival funtion is printed only each two years of age and if
         }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         /*printf("%s %s %s\n", stra,strb,modelsav);       results. So we changed our mind and took the option of the best precision.
 printf("%d ",Tvar[1]);    */
 scanf("%d",i);*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       }  
     }    agelim=AGESUP;
    else {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       for(i=j; i>=1;i--){      /* nhstepm age range expressed in number of stepm */
         cutv(stra,strb,modelsav,'+');      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
         /*printf("%s %s %s\n", stra,strb,modelsav);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           scanf("%d",i);*/      /* if (stepm >= YEARM) hstepm=1;*/
         if (strchr(strb,'*')) {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           cutv(strd,strc,strb,'*');      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           if (strcmp(strc,"age")==0) {      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
             cptcovprod--;      gp=matrix(0,nhstepm,1,nlstate*nlstate);
             cutv(strb,stre,strd,'V');      gm=matrix(0,nhstepm,1,nlstate*nlstate);
             Tvar[i+1]=atoi(stre);  
             cptcovage++;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
             Tage[cptcovage]=i+1;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
             printf("stre=%s ", stre);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
           }   
           else if (strcmp(strd,"age")==0) {  
             cptcovprod--;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
             cutv(strb,stre,strc,'V');  
             Tvar[i+1]=atoi(stre);      /* Computing Variances of health expectancies */
             cptcovage++;  
             Tage[cptcovage]=i+1;       for(theta=1; theta <=npar; theta++){
           }        for(i=1; i<=npar; i++){ 
           else {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             cutv(strb,stre,strc,'V');        }
             Tvar[i+1]=ncov+k1;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
             cutv(strb,strc,strd,'V');    
             Tprod[k1]=i+1;        cptj=0;
             Tvard[k1][1]=atoi(strc);        for(j=1; j<= nlstate; j++){
             Tvard[k1][2]=atoi(stre);          for(i=1; i<=nlstate; i++){
             Tvar[cptcovn+k2]=Tvard[k1][1];            cptj=cptj+1;
             Tvar[cptcovn+k2+1]=Tvard[k1][2];            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
             for (k=1; k<=lastobs;k++)              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
               covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];            }
             k1++;          }
             k2=k2+2;        }
           }       
         }       
         else {        for(i=1; i<=npar; i++) 
           cutv(strd,strc,strb,'V');          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           /* printf("%s %s %s", strd,strc,strb);*/        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           Tvar[i+1]=atoi(strc);        
         }        cptj=0;
         strcpy(modelsav,stra);          for(j=1; j<= nlstate; j++){
       }          for(i=1;i<=nlstate;i++){
       cutv(strd,strc,stra,'V');            cptj=cptj+1;
       Tvar[1]=atoi(strc);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     }              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   }            }
   /* for (i=1; i<=5; i++)          }
      printf("i=%d %d ",i,Tvar[i]);*/        }
   /* printf("tvar=%d %d cptcovage=%d %d",Tvar[1],Tvar[2],cptcovage,Tage[1]);*/        for(j=1; j<= nlstate*nlstate; j++)
  /*printf("cptcovprod=%d ", cptcovprod);*/          for(h=0; h<=nhstepm-1; h++){
   /*  scanf("%d ",i);*/            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     fclose(fic);          }
        } 
     /*  if(mle==1){*/     
     if (weightopt != 1) { /* Maximisation without weights*/  /* End theta */
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     /*-calculation of age at interview from date of interview and age at death -*/  
     agev=matrix(1,maxwav,1,imx);       for(h=0; h<=nhstepm-1; h++)
            for(j=1; j<=nlstate*nlstate;j++)
     for (i=1; i<=imx; i++)  {          for(theta=1; theta <=npar; theta++)
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);            trgradg[h][j][theta]=gradg[h][theta][j];
       for(m=1; (m<= maxwav); m++){       
         if(s[m][i] >0){  
           if (s[m][i] == nlstate+1) {       for(i=1;i<=nlstate*nlstate;i++)
             if(agedc[i]>0)        for(j=1;j<=nlstate*nlstate;j++)
               if(moisdc[i]!=99 && andc[i]!=9999)          varhe[i][j][(int)age] =0.;
               agev[m][i]=agedc[i];  
             else{       printf("%d|",(int)age);fflush(stdout);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
               agev[m][i]=-1;       for(h=0;h<=nhstepm-1;h++){
             }        for(k=0;k<=nhstepm-1;k++){
           }          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           else if(s[m][i] !=9){ /* Should no more exist */          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          for(i=1;i<=nlstate*nlstate;i++)
             if(mint[m][i]==99 || anint[m][i]==9999)            for(j=1;j<=nlstate*nlstate;j++)
               agev[m][i]=1;              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
             else if(agev[m][i] <agemin){        }
               agemin=agev[m][i];      }
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      /* Computing expectancies */
             }      for(i=1; i<=nlstate;i++)
             else if(agev[m][i] >agemax){        for(j=1; j<=nlstate;j++)
               agemax=agev[m][i];          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             }            
             /*agev[m][i]=anint[m][i]-annais[i];*/  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
             /*   agev[m][i] = age[i]+2*m;*/  
           }          }
           else { /* =9 */  
             agev[m][i]=1;      fprintf(ficreseij,"%3.0f",age );
             s[m][i]=-1;      cptj=0;
           }      for(i=1; i<=nlstate;i++)
         }        for(j=1; j<=nlstate;j++){
         else /*= 0 Unknown */          cptj++;
           agev[m][i]=1;          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
       }        }
          fprintf(ficreseij,"\n");
     }     
     for (i=1; i<=imx; i++)  {      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       for(m=1; (m<= maxwav); m++){      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
         if (s[m][i] > (nlstate+ndeath)) {      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
           printf("Error: Wrong value in nlstate or ndeath\n");        free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
           goto end;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }    }
       }    printf("\n");
     }    fprintf(ficlog,"\n");
   
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_vector(severity,1,maxwav);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_imatrix(outcome,1,maxwav+1,1,n);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     free_vector(moisnais,1,n);  }
     free_vector(annais,1,n);  
     free_matrix(mint,1,maxwav,1,n);  /************ Variance ******************/
     free_matrix(anint,1,maxwav,1,n);  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
     free_vector(moisdc,1,n);  {
     free_vector(andc,1,n);    /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
        /* double **newm;*/
     wav=ivector(1,imx);    double **dnewm,**doldm;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    double **dnewmp,**doldmp;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    int i, j, nhstepm, hstepm, h, nstepm ;
        int k, cptcode;
     /* Concatenates waves */    double *xp;
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
       Tcode=ivector(1,100);    double *gpp, *gmp; /* for var p point j */
       nbcode=imatrix(1,nvar,1,8);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       ncodemax[1]=1;    double ***p3mat;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    double age,agelim, hf;
          double ***mobaverage;
    codtab=imatrix(1,100,1,10);    int theta;
    h=0;    char digit[4];
    m=pow(2,cptcoveff);    char digitp[25];
    
    for(k=1;k<=cptcoveff; k++){    char fileresprobmorprev[FILENAMELENGTH];
      for(i=1; i <=(m/pow(2,k));i++){  
        for(j=1; j <= ncodemax[k]; j++){    if(popbased==1){
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      if(mobilav!=0)
            h++;        strcpy(digitp,"-populbased-mobilav-");
            if (h>m) h=1;codtab[h][k]=j;      else strcpy(digitp,"-populbased-nomobil-");
          }    }
        }    else 
      }      strcpy(digitp,"-stablbased-");
    }  
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    /*for(i=1; i <=m ;i++){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
      for(k=1; k <=cptcovn; k++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
      }      }
      printf("\n");    }
    }  
    scanf("%d",i);*/    strcpy(fileresprobmorprev,"prmorprev"); 
        sprintf(digit,"%-d",ij);
    /* Calculates basic frequencies. Computes observed prevalence at single age    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
        and prints on file fileres'p'. */    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
        fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     /* For Powell, parameters are in a vector p[] starting at p[1]    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
     if(mle==1){      for(i=1; i<=nlstate;i++)
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }    }  
        fprintf(ficresprobmorprev,"\n");
     /*--------- results files --------------*/    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
          fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
    jk=1;      exit(0);
    fprintf(ficres,"# Parameters\n");    }
    printf("# Parameters\n");    else{
    for(i=1,jk=1; i <=nlstate; i++){      fprintf(ficgp,"\n# Routine varevsij");
      for(k=1; k <=(nlstate+ndeath); k++){    }
        if (k != i)    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
          {      printf("Problem with html file: %s\n", optionfilehtm);
            printf("%d%d ",i,k);      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
            fprintf(ficres,"%1d%1d ",i,k);      exit(0);
            for(j=1; j <=ncovmodel; j++){    }
              printf("%f ",p[jk]);    else{
              fprintf(ficres,"%f ",p[jk]);      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
              jk++;      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
            }    }
            printf("\n");    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
            fprintf(ficres,"\n");  
          }    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
      }    fprintf(ficresvij,"# Age");
    }    for(i=1; i<=nlstate;i++)
  if(mle==1){      for(j=1; j<=nlstate;j++)
     /* Computing hessian and covariance matrix */        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     ftolhess=ftol; /* Usually correct */    fprintf(ficresvij,"\n");
     hesscov(matcov, p, npar, delti, ftolhess, func);  
  }    xp=vector(1,npar);
     fprintf(ficres,"# Scales\n");    dnewm=matrix(1,nlstate,1,npar);
     printf("# Scales\n");    doldm=matrix(1,nlstate,1,nlstate);
      for(i=1,jk=1; i <=nlstate; i++){    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
       for(j=1; j <=nlstate+ndeath; j++){    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         if (j!=i) {  
           fprintf(ficres,"%1d%1d",i,j);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
           printf("%1d%1d",i,j);    gpp=vector(nlstate+1,nlstate+ndeath);
           for(k=1; k<=ncovmodel;k++){    gmp=vector(nlstate+1,nlstate+ndeath);
             printf(" %.5e",delti[jk]);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
             fprintf(ficres," %.5e",delti[jk]);    
             jk++;    if(estepm < stepm){
           }      printf ("Problem %d lower than %d\n",estepm, stepm);
           printf("\n");    }
           fprintf(ficres,"\n");    else  hstepm=estepm;   
         }    /* For example we decided to compute the life expectancy with the smallest unit */
       }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       }       nhstepm is the number of hstepm from age to agelim 
           nstepm is the number of stepm from age to agelin. 
     k=1;       Look at hpijx to understand the reason of that which relies in memory size
     fprintf(ficres,"# Covariance\n");       and note for a fixed period like k years */
     printf("# Covariance\n");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     for(i=1;i<=npar;i++){       survival function given by stepm (the optimization length). Unfortunately it
       /*  if (k>nlstate) k=1;       means that if the survival funtion is printed every two years of age and if
       i1=(i-1)/(ncovmodel*nlstate)+1;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);       results. So we changed our mind and took the option of the best precision.
       printf("%s%d%d",alph[k],i1,tab[i]);*/    */
       fprintf(ficres,"%3d",i);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       printf("%3d",i);    agelim = AGESUP;
       for(j=1; j<=i;j++){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         fprintf(ficres," %.5e",matcov[i][j]);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         printf(" %.5e",matcov[i][j]);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficres,"\n");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       printf("\n");      gp=matrix(0,nhstepm,1,nlstate);
       k++;      gm=matrix(0,nhstepm,1,nlstate);
     }  
      
     while((c=getc(ficpar))=='#' && c!= EOF){      for(theta=1; theta <=npar; theta++){
       ungetc(c,ficpar);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       fgets(line, MAXLINE, ficpar);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       puts(line);        }
       fputs(line,ficparo);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     ungetc(c,ficpar);  
          if (popbased==1) {
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);          if(mobilav ==0){
                for(i=1; i<=nlstate;i++)
     if (fage <= 2) {              prlim[i][i]=probs[(int)age][i][ij];
       bage = agemin;          }else{ /* mobilav */ 
       fage = agemax;            for(i=1; i<=nlstate;i++)
     }              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");        }
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    
         for(j=1; j<= nlstate; j++){
              for(h=0; h<=nhstepm; h++){
 /*------------ gnuplot -------------*/            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
 chdir(pathcd);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   if((ficgp=fopen("graph.plt","w"))==NULL) {          }
     printf("Problem with file graph.gp");goto end;        }
   }        /* This for computing probability of death (h=1 means
 #ifdef windows           computed over hstepm matrices product = hstepm*stepm months) 
   fprintf(ficgp,"cd \"%s\" \n",pathc);           as a weighted average of prlim.
 #endif        */
 m=pow(2,cptcoveff);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
            for(i=1,gpp[j]=0.; i<= nlstate; i++)
  /* 1eme*/            gpp[j] += prlim[i][i]*p3mat[i][j][1];
   for (cpt=1; cpt<= nlstate ; cpt ++) {        }    
    for (k1=1; k1<= m ; k1 ++) {        /* end probability of death */
   
 #ifdef windows        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 #endif        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 #ifdef unix        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);   
 #endif        if (popbased==1) {
           if(mobilav ==0){
 for (i=1; i<= nlstate ; i ++) {            for(i=1; i<=nlstate;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              prlim[i][i]=probs[(int)age][i][ij];
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }else{ /* mobilav */ 
 }            for(i=1; i<=nlstate;i++)
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);              prlim[i][i]=mobaverage[(int)age][i][ij];
     for (i=1; i<= nlstate ; i ++) {          }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }        for(j=1; j<= nlstate; j++){
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          for(h=0; h<=nhstepm; h++){
      for (i=1; i<= nlstate ; i ++) {            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }          }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        /* This for computing probability of death (h=1 means
 #ifdef unix           computed over hstepm matrices product = hstepm*stepm months) 
 fprintf(ficgp,"\nset ter gif small size 400,300");           as a weighted average of prlim.
 #endif        */
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
    }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   /*2 eme*/        }    
         /* end probability of death */
   for (k1=1; k1<= m ; k1 ++) {  
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);        for(j=1; j<= nlstate; j++) /* vareij */
              for(h=0; h<=nhstepm; h++){
     for (i=1; i<= nlstate+1 ; i ++) {            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       k=2*i;          }
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }    
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      } /* End theta */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      for(h=0; h<=nhstepm; h++) /* veij */
         else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=1; j<=nlstate;j++)
 }            for(theta=1; theta <=npar; theta++)
       fprintf(ficgp,"\" t\"\" w l 0,");            trgradg[h][j][theta]=gradg[h][theta][j];
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(theta=1; theta <=npar; theta++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");          trgradgp[j][theta]=gradgp[theta][j];
 }      
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  
       else fprintf(ficgp,"\" t\"\" w l 0,");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     }      for(i=1;i<=nlstate;i++)
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        for(j=1;j<=nlstate;j++)
   }          vareij[i][j][(int)age] =0.;
    
   /*3eme*/      for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
   for (k1=1; k1<= m ; k1 ++) {          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     for (cpt=1; cpt<= nlstate ; cpt ++) {          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       k=2+nlstate*(cpt-1);          for(i=1;i<=nlstate;i++)
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);            for(j=1;j<=nlstate;j++)
       for (i=1; i< nlstate ; i ++) {              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);        }
       }      }
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    
     }      /* pptj */
   }      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
        matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   /* CV preval stat */      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   for (k1=1; k1<= m ; k1 ++) {        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     for (cpt=1; cpt<nlstate ; cpt ++) {          varppt[j][i]=doldmp[j][i];
       k=3;      /* end ppptj */
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);      /*  x centered again */
       for (i=1; i< nlstate ; i ++)      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficgp,"+$%d",k+i+1);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);   
            if (popbased==1) {
       l=3+(nlstate+ndeath)*cpt;        if(mobilav ==0){
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          for(i=1; i<=nlstate;i++)
       for (i=1; i< nlstate ; i ++) {            prlim[i][i]=probs[(int)age][i][ij];
         l=3+(nlstate+ndeath)*cpt;        }else{ /* mobilav */ 
         fprintf(ficgp,"+$%d",l+i+1);          for(i=1; i<=nlstate;i++)
       }            prlim[i][i]=mobaverage[(int)age][i][ij];
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          }
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      }
     }               
   }      /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   /* proba elementaires */         as a weighted average of prlim.
    for(i=1,jk=1; i <=nlstate; i++){      */
     for(k=1; k <=(nlstate+ndeath); k++){      for(j=nlstate+1;j<=nlstate+ndeath;j++){
       if (k != i) {        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
         for(j=1; j <=ncovmodel; j++){          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/      }    
           /*fprintf(ficgp,"%s",alph[1]);*/      /* end probability of death */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  
           jk++;      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
           fprintf(ficgp,"\n");      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         }        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       }        for(i=1; i<=nlstate;i++){
     }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     }        }
       } 
   for(jk=1; jk <=m; jk++) {      fprintf(ficresprobmorprev,"\n");
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);  
    i=1;      fprintf(ficresvij,"%.0f ",age );
    for(k2=1; k2<=nlstate; k2++) {      for(i=1; i<=nlstate;i++)
      k3=i;        for(j=1; j<=nlstate;j++){
      for(k=1; k<=(nlstate+ndeath); k++) {          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
        if (k != k2){        }
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      fprintf(ficresvij,"\n");
 ij=1;      free_matrix(gp,0,nhstepm,1,nlstate);
         for(j=3; j <=ncovmodel; j++) {      free_matrix(gm,0,nhstepm,1,nlstate);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
             ij++;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }    } /* End age */
           else    free_vector(gpp,nlstate+1,nlstate+ndeath);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    free_vector(gmp,nlstate+1,nlstate+ndeath);
         }    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
           fprintf(ficgp,")/(1");    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
            fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
         for(k1=1; k1 <=nlstate; k1++){      /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
 ij=1;  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
           for(j=3; j <=ncovmodel; j++){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
             ij++;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
           }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
           else    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
           }    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
           fprintf(ficgp,")");  */
         }    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);  
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    free_vector(xp,1,npar);
         i=i+ncovmodel;    free_matrix(doldm,1,nlstate,1,nlstate);
        }    free_matrix(dnewm,1,nlstate,1,npar);
      }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    }    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        fclose(ficresprobmorprev);
   fclose(ficgp);    fclose(ficgp);
        fclose(fichtm);
 chdir(path);  }  
     free_matrix(agev,1,maxwav,1,imx);  
     free_ivector(wav,1,imx);  /************ Variance of prevlim ******************/
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);  {
        /* Variance of prevalence limit */
     free_imatrix(s,1,maxwav+1,1,n);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
        double **newm;
        double **dnewm,**doldm;
     free_ivector(num,1,n);    int i, j, nhstepm, hstepm;
     free_vector(agedc,1,n);    int k, cptcode;
     free_vector(weight,1,n);    double *xp;
     /*free_matrix(covar,1,NCOVMAX,1,n);*/    double *gp, *gm;
     fclose(ficparo);    double **gradg, **trgradg;
     fclose(ficres);    double age,agelim;
     /*  }*/    int theta;
         
    /*________fin mle=1_________*/    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
        fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
          fprintf(ficresvpl," %1d-%1d",i,i);
     /* No more information from the sample is required now */    fprintf(ficresvpl,"\n");
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    xp=vector(1,npar);
     ungetc(c,ficpar);    dnewm=matrix(1,nlstate,1,npar);
     fgets(line, MAXLINE, ficpar);    doldm=matrix(1,nlstate,1,nlstate);
     puts(line);    
     fputs(line,ficparo);    hstepm=1*YEARM; /* Every year of age */
   }    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   ungetc(c,ficpar);    agelim = AGESUP;
      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);      if (stepm >= YEARM) hstepm=1;
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
 /*--------- index.htm --------*/      gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
   if((fichtm=fopen("index.htm","w"))==NULL)    {      gm=vector(1,nlstate);
     printf("Problem with index.htm \n");goto end;  
   }      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
  fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        }
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>        for(i=1;i<=nlstate;i++)
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>          gp[i] = prlim[i][i];
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>      
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>        for(i=1; i<=npar; i++) /* Computes gradient */
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);        for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
  fprintf(fichtm," <li>Graphs</li>\n<p>");  
         for(i=1;i<=nlstate;i++)
  m=cptcoveff;          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      } /* End theta */
   
  j1=0;      trgradg =matrix(1,nlstate,1,npar);
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){      for(j=1; j<=nlstate;j++)
        j1++;        for(theta=1; theta <=npar; theta++)
        if (cptcovn > 0) {          trgradg[j][theta]=gradg[theta][j];
          fprintf(fichtm,"<hr>************ Results for covariates");  
          for (cpt=1; cpt<=cptcoveff;cpt++)      for(i=1;i<=nlstate;i++)
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);        varpl[i][(int)age] =0.;
          fprintf(fichtm," ************\n<hr>");      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
        }      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      for(i=1;i<=nlstate;i++)
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
        for(cpt=1; cpt<nlstate;cpt++){  
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      fprintf(ficresvpl,"%.0f ",age );
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      for(i=1; i<=nlstate;i++)
        }        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
     for(cpt=1; cpt<=nlstate;cpt++) {      fprintf(ficresvpl,"\n");
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      free_vector(gp,1,nlstate);
 interval) in state (%d): v%s%d%d.gif <br>      free_vector(gm,1,nlstate);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        free_matrix(gradg,1,npar,1,nlstate);
      }      free_matrix(trgradg,1,nlstate,1,npar);
      for(cpt=1; cpt<=nlstate;cpt++) {    } /* End age */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>  
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    free_vector(xp,1,npar);
      }    free_matrix(doldm,1,nlstate,1,npar);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    free_matrix(dnewm,1,nlstate,1,nlstate);
 health expectancies in states (1) and (2): e%s%d.gif<br>  
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);  }
 fprintf(fichtm,"\n</body>");  
    }  /************ Variance of one-step probabilities  ******************/
  }  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
 fclose(fichtm);  {
     int i, j=0,  i1, k1, l1, t, tj;
   /*--------------- Prevalence limit --------------*/    int k2, l2, j1,  z1;
      int k=0,l, cptcode;
   strcpy(filerespl,"pl");    int first=1, first1;
   strcat(filerespl,fileres);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    double **dnewm,**doldm;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    double *xp;
   }    double *gp, *gm;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    double **gradg, **trgradg;
   fprintf(ficrespl,"#Prevalence limit\n");    double **mu;
   fprintf(ficrespl,"#Age ");    double age,agelim, cov[NCOVMAX];
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   fprintf(ficrespl,"\n");    int theta;
      char fileresprob[FILENAMELENGTH];
   prlim=matrix(1,nlstate,1,nlstate);    char fileresprobcov[FILENAMELENGTH];
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    char fileresprobcor[FILENAMELENGTH];
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double ***varpij;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    strcpy(fileresprob,"prob"); 
   k=0;    strcat(fileresprob,fileres);
   agebase=agemin;    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   agelim=agemax;      printf("Problem with resultfile: %s\n", fileresprob);
   ftolpl=1.e-10;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   i1=cptcoveff;    }
   if (cptcovn < 1){i1=1;}    strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
   for(cptcov=1;cptcov<=i1;cptcov++){    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      printf("Problem with resultfile: %s\n", fileresprobcov);
         k=k+1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    }
         fprintf(ficrespl,"\n#******");    strcpy(fileresprobcor,"probcor"); 
         for(j=1;j<=cptcoveff;j++)    strcat(fileresprobcor,fileres);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
         fprintf(ficrespl,"******\n");      printf("Problem with resultfile: %s\n", fileresprobcor);
              fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
         for (age=agebase; age<=agelim; age++){    }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           fprintf(ficrespl,"%.0f",age );    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           for(i=1; i<=nlstate;i++)    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           fprintf(ficrespl," %.5f", prlim[i][i]);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           fprintf(ficrespl,"\n");    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         }    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       }    
     }    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   fclose(ficrespl);    fprintf(ficresprob,"# Age");
   /*------------- h Pij x at various ages ------------*/    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
      fprintf(ficresprobcov,"# Age");
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    fprintf(ficresprobcov,"# Age");
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  
   }  
   printf("Computing pij: result on file '%s' \n", filerespij);    for(i=1; i<=nlstate;i++)
        for(j=1; j<=(nlstate+ndeath);j++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   if (stepm<=24) stepsize=2;        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
   agelim=AGESUP;      }  
   hstepm=stepsize*YEARM; /* Every year of age */   /* fprintf(ficresprob,"\n");
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    fprintf(ficresprobcov,"\n");
      fprintf(ficresprobcor,"\n");
   k=0;   */
   for(cptcov=1;cptcov<=i1;cptcov++){   xp=vector(1,npar);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       k=k+1;    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
         fprintf(ficrespij,"\n#****** ");    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
         for(j=1;j<=cptcoveff;j++)    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    first=1;
         fprintf(ficrespij,"******\n");    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
              printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      exit(0);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    else{
           oldm=oldms;savm=savms;      fprintf(ficgp,"\n# Routine varprob");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      }
           fprintf(ficrespij,"# Age");    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
           for(i=1; i<=nlstate;i++)      printf("Problem with html file: %s\n", optionfilehtm);
             for(j=1; j<=nlstate+ndeath;j++)      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
               fprintf(ficrespij," %1d-%1d",i,j);      exit(0);
           fprintf(ficrespij,"\n");    }
           for (h=0; h<=nhstepm; h++){    else{
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
             for(i=1; i<=nlstate;i++)      fprintf(fichtm,"\n");
               for(j=1; j<=nlstate+ndeath;j++)  
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
             fprintf(ficrespij,"\n");      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
           }      fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");    }
         }  
     }    cov[1]=1;
   }    tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   fclose(ficrespij);    j1=0;
     for(t=1; t<=tj;t++){
   /*---------- Health expectancies and variances ------------*/      for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
   strcpy(filerest,"t");        if  (cptcovn>0) {
   strcat(filerest,fileres);          fprintf(ficresprob, "\n#********** Variable "); 
   if((ficrest=fopen(filerest,"w"))==NULL) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;          fprintf(ficresprob, "**********\n#\n");
   }          fprintf(ficresprobcov, "\n#********** Variable "); 
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
   strcpy(filerese,"e");          fprintf(ficgp, "\n#********** Variable "); 
   strcat(filerese,fileres);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if((ficreseij=fopen(filerese,"w"))==NULL) {          fprintf(ficgp, "**********\n#\n");
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          
   }          
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  strcpy(fileresv,"v");          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   strcat(fileresv,fileres);          
   if((ficresvij=fopen(fileresv,"w"))==NULL) {          fprintf(ficresprobcor, "\n#********** Variable ");    
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(ficresprobcor, "**********\n#");    
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        }
         
   k=0;        for (age=bage; age<=fage; age ++){ 
   for(cptcov=1;cptcov<=i1;cptcov++){          cov[2]=age;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for (k=1; k<=cptcovn;k++) {
       k=k+1;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
       fprintf(ficrest,"\n#****** ");          }
       for(j=1;j<=cptcoveff;j++)          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for (k=1; k<=cptcovprod;k++)
       fprintf(ficrest,"******\n");            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       fprintf(ficreseij,"\n#****** ");          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       for(j=1;j<=cptcoveff;j++)          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          gp=vector(1,(nlstate)*(nlstate+ndeath));
       fprintf(ficreseij,"******\n");          gm=vector(1,(nlstate)*(nlstate+ndeath));
       
       fprintf(ficresvij,"\n#****** ");          for(theta=1; theta <=npar; theta++){
       for(j=1;j<=cptcoveff;j++)            for(i=1; i<=npar; i++)
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       fprintf(ficresvij,"******\n");            
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            
       oldm=oldms;savm=savms;            k=0;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);              for(i=1; i<= (nlstate); i++){
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);              for(j=1; j<=(nlstate+ndeath);j++){
       oldm=oldms;savm=savms;                k=k+1;
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                gp[k]=pmmij[i][j];
                    }
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");            }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);            
       fprintf(ficrest,"\n");            for(i=1; i<=npar; i++)
                      xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       hf=1;      
       if (stepm >= YEARM) hf=stepm/YEARM;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       epj=vector(1,nlstate+1);            k=0;
       for(age=bage; age <=fage ;age++){            for(i=1; i<=(nlstate); i++){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);              for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficrest," %.0f",age);                k=k+1;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                gm[k]=pmmij[i][j];
           for(i=1, epj[j]=0.;i <=nlstate;i++) {              }
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];            }
           }       
           epj[nlstate+1] +=epj[j];            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
         }              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
         for(i=1, vepp=0.;i <=nlstate;i++)          }
           for(j=1;j <=nlstate;j++)  
             vepp += vareij[i][j][(int)age];          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));            for(theta=1; theta <=npar; theta++)
         for(j=1;j <=nlstate;j++){              trgradg[j][theta]=gradg[theta][j];
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));          
         }          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
         fprintf(ficrest,"\n");          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       }          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     }          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   }          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                  free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
  fclose(ficreseij);  
  fclose(ficresvij);          pmij(pmmij,cov,ncovmodel,x,nlstate);
   fclose(ficrest);          
   fclose(ficpar);          k=0;
   free_vector(epj,1,nlstate+1);          for(i=1; i<=(nlstate); i++){
   /*  scanf("%d ",i); */            for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
   /*------- Variance limit prevalence------*/                mu[k][(int) age]=pmmij[i][j];
             }
 strcpy(fileresvpl,"vpl");          }
   strcat(fileresvpl,fileres);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);              varpij[i][j][(int)age] = doldm[i][j];
     exit(0);  
   }          /*printf("\n%d ",(int)age);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
  k=0;            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
  for(cptcov=1;cptcov<=i1;cptcov++){            }*/
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
      k=k+1;          fprintf(ficresprob,"\n%d ",(int)age);
      fprintf(ficresvpl,"\n#****** ");          fprintf(ficresprobcov,"\n%d ",(int)age);
      for(j=1;j<=cptcoveff;j++)          fprintf(ficresprobcor,"\n%d ",(int)age);
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
      fprintf(ficresvpl,"******\n");          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                  fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
      varpl=matrix(1,nlstate,(int) bage, (int) fage);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
      oldm=oldms;savm=savms;            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
    }          }
  }          i=0;
           for (k=1; k<=(nlstate);k++){
   fclose(ficresvpl);            for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
   /*---------- End : free ----------------*/              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                for (j=1; j<=i;j++){
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                }
              }
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          }/* end of loop for state */
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        } /* end of loop for age */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        /* Confidence intervalle of pij  */
          /*
   free_matrix(matcov,1,npar,1,npar);          fprintf(ficgp,"\nset noparametric;unset label");
   free_vector(delti,1,npar);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
            fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   printf("End of Imach\n");          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
          */
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/  
   /*printf("Total time was %d uSec.\n", total_usecs);*/        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   /*------ End -----------*/        first1=1;
         for (k2=1; k2<=(nlstate);k2++){
  end:          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
 #ifdef windows            if(l2==k2) continue;
  chdir(pathcd);            j=(k2-1)*(nlstate+ndeath)+l2;
 #endif            for (k1=1; k1<=(nlstate);k1++){
  system("wgnuplot graph.plt");              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
 #ifdef windows                i=(k1-1)*(nlstate+ndeath)+l1;
   while (z[0] != 'q') {                if(i<=j) continue;
     chdir(pathcd);                for (age=bage; age<=fage; age ++){ 
     printf("\nType e to edit output files, c to start again, and q for exiting: ");                  if ((int)age %5==0){
     scanf("%s",z);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     if (z[0] == 'c') system("./imach");                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     else if (z[0] == 'e') {                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
       chdir(path);                    mu1=mu[i][(int) age]/stepm*YEARM ;
       system("index.htm");                    mu2=mu[j][(int) age]/stepm*YEARM;
     }                    c12=cv12/sqrt(v1*v2);
     else if (z[0] == 'q') exit(0);                    /* Computing eigen value of matrix of covariance */
   }                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
 #endif                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
 }                    /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtm," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fclose(ficgp);
     fclose(fichtm);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
     /*char optionfilehtm[FILENAMELENGTH];*/
     if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
       fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
     }
   
      fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
    - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
    - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
    - Life expectancies by age and initial health status (estepm=%2d months): 
      <a href=\"e%s\">e%s</a> <br>\n</li>", \
     jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
   <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
   <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
          /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
   <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
   <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and
   health expectancies in states (1) and (2): e%s%d.png<br>
   <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
    - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
    - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
    - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
    - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
    - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
   
    if(popforecast==1) fprintf(fichtm,"\n
    - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
    - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
           <br>",fileres,fileres,fileres,fileres);
    else 
      fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
   interval) in state (%d): v%s%d%d.png <br>
   <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   fclose(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
       fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     }
   
     /*#ifdef windows */
       fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   m=pow(2,cptcoveff);
     
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stat */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fclose(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (YEARM*yearp)) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h==(int)(YEARM*yearp))
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                 }
                 if (h==(int)(YEARM*yearp)){
                   fprintf(ficresf," %.3f", ppij);
                 }
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
       }
     }
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   }
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   #include <sys/time.h>
   #include <time.h>
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
    
     /* long total_usecs;
        struct timeval start_time, end_time;
     
        gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     getcwd(pathcd, size);
   
     printf("\n%s",version);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     replace(pathc,path);
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s",version);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       goto end;
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
         }
         else
           fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if(moisdc[i]!=99 && andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if (andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if(mint[m][i]==99 || anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
      fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting: %s\n",plotcmd);fflush(stdout);
     system(plotcmd);
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

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changed lines
  Added in v.1.74


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